diff --git a/erpnext/accounts/doctype/payment_reconciliation/payment_reconciliation.js b/erpnext/accounts/doctype/payment_reconciliation/payment_reconciliation.js
index 14520c2..c495a35 100644
--- a/erpnext/accounts/doctype/payment_reconciliation/payment_reconciliation.js
+++ b/erpnext/accounts/doctype/payment_reconciliation/payment_reconciliation.js
@@ -7,22 +7,40 @@
 
 	onload: function() {
 		var me = this
-		this.frm.set_query ('party_account', function() {
-			return{
-				filters:[
-					['Account', 'company', '=', me.frm.doc.company],
-					['Account', 'group_or_ledger', '=', 'Ledger'],
-					['Account', 'master_type', 'in', ['Customer', 'Supplier']]
-				]
-			};
+		this.frm.set_query('party_account', function() {
+			if(!me.frm.doc.company) {
+				msgprint(__("Please select company first"));
+			} else {
+				return{
+					filters:[
+						['Account', 'company', '=', me.frm.doc.company],
+						['Account', 'group_or_ledger', '=', 'Ledger'],
+						['Account', 'master_type', 'in', ['Customer', 'Supplier']]
+					]
+				};
+			}
+			
+		});
+		
+		this.frm.set_query('bank_cash_account', function() {
+			if(!me.frm.doc.company) {
+				msgprint(__("Please select company first"));
+			} else {
+				return{
+					filters:[
+						['Account', 'company', '=', me.frm.doc.company],
+						['Account', 'group_or_ledger', '=', 'Ledger'],
+						['Account', 'account_type', 'in', ['Bank', 'Cash']]
+					]
+				};
+			}
 		});
 
-		var help_content = ['<i class="icon-hand-right"></i> Note:',
-		'<ul>If you are unable to match the exact amount, then amend your Journal Voucher and split rows such that your amounts match the invoice you are trying to reconcile. </ul>'].join("\n");
+		var help_content = '<i class="icon-hand-right"></i> Note:<br>'+
+			'<ul>If you are unable to match the exact amount, then amend your Journal Voucher and split rows such that payment amount match the invoice amount.</ul>';
 		this.frm.set_value("reconcile_help", help_content);
 	},
-
-
+	
 	get_unreconciled_entries: function() {
 		var me = this;
 		return this.frm.call({
diff --git a/erpnext/accounts/doctype/payment_reconciliation/payment_reconciliation.json b/erpnext/accounts/doctype/payment_reconciliation/payment_reconciliation.json
index 40b5706..a83d453 100644
--- a/erpnext/accounts/doctype/payment_reconciliation/payment_reconciliation.json
+++ b/erpnext/accounts/doctype/payment_reconciliation/payment_reconciliation.json
@@ -31,7 +31,7 @@
    "hidden": 1, 
    "in_list_view": 1, 
    "label": "Party Type", 
-   "options": "Customer\nSupplier", 
+   "options": "\nCustomer\nSupplier", 
    "permlevel": 0, 
    "read_only": 1, 
    "reqd": 0
@@ -129,7 +129,7 @@
  ], 
  "hide_toolbar": 1, 
  "issingle": 1, 
- "modified": "2014-07-18 15:53:20.638456", 
+ "modified": "2014-07-21 16:54:31.454679", 
  "modified_by": "Administrator", 
  "module": "Accounts", 
  "name": "Payment Reconciliation", 
diff --git a/erpnext/accounts/doctype/payment_reconciliation/payment_reconciliation.py b/erpnext/accounts/doctype/payment_reconciliation/payment_reconciliation.py
index be53aca..2d844bb 100644
--- a/erpnext/accounts/doctype/payment_reconciliation/payment_reconciliation.py
+++ b/erpnext/accounts/doctype/payment_reconciliation/payment_reconciliation.py
@@ -18,7 +18,12 @@
 	def get_jv_entries(self):
 		self.check_mandatory_to_fetch()
 		dr_or_cr = "credit" if self.party_type == "Customer" else "debit"
-		cond = self.check_condition(dr_or_cr)
+		if self.party_type=="Customer":
+			amount_query = "ifnull(t2.credit, 0) - ifnull(t2.debit, 0)"
+		else:
+			amount_query = "ifnull(t2.debit, 0) - ifnull(t2.credit, 0)"
+			
+		cond = self.check_condition(amount_query)
 
 		bank_account_condition = "t2.against_account like %(bank_cash_account)s" \
 				if self.bank_cash_account else "1=1"
@@ -26,22 +31,26 @@
 		jv_entries = frappe.db.sql("""
 			select
 				t1.name as voucher_no, t1.posting_date, t1.remark, t2.account, 
-				t2.name as voucher_detail_no,  t2.{dr_or_cr}, t2.is_advance
+				t2.name as voucher_detail_no, {amount_query} as payment_amount, t2.is_advance
 			from
 				`tabJournal Voucher` t1, `tabJournal Voucher Detail` t2
 			where
-				t1.name = t2.parent and t1.docstatus = 1 and t2.account = %(party_account)s
-				and t2.{dr_or_cr} > 0 and ifnull(t2.against_voucher, '')='' and ifnull(t2.against_invoice, '')='' 
+				t1.name = t2.parent and t1.docstatus = 1 and t2.docstatus = 1
+				and t2.account = %(party_account)s and {amount_query} > 0 
+				and ifnull((select ifnull(sum(ifnull(credit, 0) - ifnull(debit, 0)), 0) from `tabJournal Voucher Detail` 
+					where parent=t1.name and account=t2.account and docstatus=1 group by account), 0) > 0
+				and ifnull(t2.against_voucher, '')='' and ifnull(t2.against_invoice, '')='' 
 				and ifnull(t2.against_jv, '')='' {cond} 
 				and (CASE
 					WHEN t1.voucher_type in ('Debit Note', 'Credit Note')
 					THEN 1=1
 					ELSE {bank_account_condition}
 				END)
-			group by t1.name, t2.name """.format(**{
+			""".format(**{
 				"dr_or_cr": dr_or_cr,
 				"cond": cond,
-				"bank_account_condition": bank_account_condition
+				"bank_account_condition": bank_account_condition,
+				"amount_query": amount_query
 			}), {
 				"party_account": self.party_account,
 				"bank_cash_account": "%%%s%%" % self.bank_cash_account
@@ -55,7 +64,7 @@
 			ent = self.append('payment_reconciliation_payments', {})
 			ent.journal_voucher = e.get('voucher_no')
 			ent.posting_date = e.get('posting_date')
-			ent.amount = flt(e.get('credit')) or flt(e.get('debit'))
+			ent.amount = flt(e.get('payment_amount'))
 			ent.remark = e.get('remark')
 			ent.voucher_detail_number = e.get('voucher_detail_no')
 			ent.is_advance = e.get('is_advance')
@@ -64,55 +73,63 @@
 		#Fetch JVs, Sales and Purchase Invoices for 'payment_reconciliation_invoices' to reconcile against
 		non_reconciled_invoices = []
 		dr_or_cr = "debit" if self.party_type == "Customer" else "credit"
-		cond = self.check_condition(dr_or_cr)
+		if self.party_type=="Customer":
+			amount_query = "ifnull(debit, 0) - ifnull(credit, 0)"
+		else:
+			amount_query = "ifnull(credit, 0) - ifnull(debit, 0)"
+		
+		cond = self.check_condition(amount_query)
 
 		invoice_list = frappe.db.sql("""
 			select
-				voucher_no, voucher_type, posting_date, ifnull(sum(ifnull(%s, 0)), 0) as amount
+				voucher_no, voucher_type, posting_date, 
+				ifnull(sum({amount_query}), 0) as invoice_amount
 			from
 				`tabGL Entry`
 			where
-				account = %s and ifnull(%s, 0) > 0 %s
-			group by voucher_no, voucher_type""" % (dr_or_cr, '%s', 
-				dr_or_cr, cond), (self.party_account), as_dict=True)
+				account = %s and {amount_query} > 0 {cond}
+			group by voucher_type, voucher_no
+		""".format(**{
+			"cond": cond,
+			"amount_query": amount_query
+		}), (self.party_account), as_dict=True)
 
 		for d in invoice_list:
 			payment_amount = frappe.db.sql("""
 				select
-					ifnull(sum(ifnull(%s, 0)), 0)
+					ifnull(sum(ifnull({amount_query}, 0)), 0)
 				from
 					`tabGL Entry`
 				where
-					account = %s and against_voucher_type = %s and ifnull(against_voucher, '') = %s""" %
-					(("credit" if self.party_type == "Customer" else "debit"), '%s', '%s', '%s'), 
-					(self.party_account, d.voucher_type, d.voucher_no)) 
+					account = %s and {amount_query} < 0 
+					and against_voucher_type = %s and ifnull(against_voucher, '') = %s
+			""".format(**{
+				"cond": cond,
+				"amount_query": amount_query
+			}), (self.party_account, d.voucher_type, d.voucher_no))
+			
+			payment_amount = -1*payment_amount[0][0] if payment_amount else 0
 
-			payment_amount = payment_amount[0][0] if payment_amount else 0
-
-			if d.amount > payment_amount:
+			if d.invoice_amount > payment_amount:
 				non_reconciled_invoices.append({
 					'voucher_no': d.voucher_no, 
 					'voucher_type': d.voucher_type, 
 					'posting_date': d.posting_date, 
-					'amount': flt(d.amount), 
-					'outstanding_amount': d.amount - payment_amount})
+					'invoice_amount': flt(d.invoice_amount), 
+					'outstanding_amount': d.invoice_amount - payment_amount})
 
 		self.add_invoice_entries(non_reconciled_invoices)
 
-
 	def add_invoice_entries(self, non_reconciled_invoices):
 		#Populate 'payment_reconciliation_invoices' with JVs and Invoices to reconcile against
 		self.set('payment_reconciliation_invoices', [])
-		if not non_reconciled_invoices:
-			frappe.throw(_("No invoices found to be reconciled"))
-
-
+		
 		for e in non_reconciled_invoices:
 			ent = self.append('payment_reconciliation_invoices', {})
 			ent.invoice_type = e.get('voucher_type')
 			ent.invoice_number = e.get('voucher_no')
 			ent.invoice_date = e.get('posting_date')
-			ent.amount = flt(e.get('amount'))
+			ent.amount = flt(e.get('invoice_amount'))
 			ent.outstanding_amount = e.get('outstanding_amount')
 
 	def reconcile(self, args):
@@ -121,24 +138,24 @@
 		dr_or_cr = "credit" if self.party_type == "Customer" else "debit"
 		lst = []
 		for e in self.get('payment_reconciliation_payments'):
-			lst.append({
-				'voucher_no' : e.journal_voucher,
-				'voucher_detail_no' : e.voucher_detail_number,
-				'against_voucher_type' : e.invoice_type,
-				'against_voucher'  : e.invoice_number,
-				'account' : self.party_account,
-				'is_advance' : e.is_advance,
-				'dr_or_cr' : dr_or_cr,
-				'unadjusted_amt' : flt(e.amount),
-				'allocated_amt' : flt(e.amount)
-			})
+			if e.invoice_type and e.invoice_number:
+				lst.append({
+					'voucher_no' : e.journal_voucher,
+					'voucher_detail_no' : e.voucher_detail_number,
+					'against_voucher_type' : e.invoice_type,
+					'against_voucher'  : e.invoice_number,
+					'account' : self.party_account,
+					'is_advance' : e.is_advance,
+					'dr_or_cr' : dr_or_cr,
+					'unadjusted_amt' : flt(e.amount),
+					'allocated_amt' : flt(e.amount)
+				})
 
 		if lst:
 			from erpnext.accounts.utils import reconcile_against_document
 			reconcile_against_document(lst)
-			self.get_unreconciled_entries()
 			msgprint(_("Successfully Reconciled"))
-
+			self.get_unreconciled_entries()
 
 	def check_mandatory_to_fetch(self):
 		for fieldname in ["company", "party_account"]:
@@ -147,32 +164,38 @@
 
 
 	def validate_invoice(self):
+		if not self.get("payment_reconciliation_invoices"):
+			frappe.throw(_("No records found in the Invoice table"))
+			
+		if not self.get("payment_reconciliation_payments"):
+			frappe.throw(_("No records found in the Payment table"))
+			
 		unreconciled_invoices = frappe._dict()
 		for d in self.get("payment_reconciliation_invoices"):
 			unreconciled_invoices.setdefault(d.invoice_type, {}).setdefault(d.invoice_number, d.outstanding_amount)
-
+		
 		invoices_to_reconcile = []
 		for p in self.get("payment_reconciliation_payments"):
 			if p.invoice_type and p.invoice_number:
 				invoices_to_reconcile.append(p.invoice_number)
 
-				if p.invoice_number not in unreconciled_invoices.get(p.invoice_type):
+				if p.invoice_number not in unreconciled_invoices.get(p.invoice_type, {}):
 					frappe.throw(_("{0}: {1} not found in Invoice Details table")
 						.format(p.invoice_type, p.invoice_number))
 
-				if p.amount > unreconciled_invoices.get(p.invoice_type).get(p.invoice_number):
-					frappe.throw(_("Row {0}: Payment amount must be less than or equals to invoice outstanding amount").format(p.idx))
+				if p.amount > unreconciled_invoices.get(p.invoice_type, {}).get(p.invoice_number):
+					frappe.throw(_("Row {0}: Payment amount must be less than or equals to invoice outstanding amount. Please refer Note below.").format(p.idx))
 
 		if not invoices_to_reconcile:
 			frappe.throw(_("Please select Invoice Type and Invoice Number in atleast one row"))
 
-	def check_condition(self, dr_or_cr):
+	def check_condition(self, amount_query):
 		cond = self.from_date and " and posting_date >= '" + self.from_date + "'" or ""
 		cond += self.to_date and " and posting_date <= '" + self.to_date + "'" or ""
 
 		if self.minimum_amount:
-			cond += " and ifnull(%s, 0) >= %s" % (dr_or_cr, self.minimum_amount) 
+			cond += " and {0} >= %s".format(amount_query) % self.minimum_amount
 		if self.maximum_amount:
-			cond += " and ifnull(%s, 0) <= %s" % (dr_or_cr, self.maximum_amount)
+			cond += " and {0} <= %s".format(amount_query) % self.maximum_amount
 
 		return cond 
\ No newline at end of file
diff --git a/erpnext/accounts/doctype/payment_reconciliation_payment/payment_reconciliation_payment.json b/erpnext/accounts/doctype/payment_reconciliation_payment/payment_reconciliation_payment.json
index 3dd36fc..73fd0f5 100644
--- a/erpnext/accounts/doctype/payment_reconciliation_payment/payment_reconciliation_payment.json
+++ b/erpnext/accounts/doctype/payment_reconciliation_payment/payment_reconciliation_payment.json
@@ -59,7 +59,7 @@
    "fieldtype": "Select", 
    "in_list_view": 1, 
    "label": "Invoice Type", 
-   "options": "Sales Invoice\nPurchase Invoice\nJournal Voucher", 
+   "options": "\nSales Invoice\nPurchase Invoice\nJournal Voucher", 
    "permlevel": 0, 
    "read_only": 0, 
    "reqd": 1
@@ -95,7 +95,7 @@
   }
  ], 
  "istable": 1, 
- "modified": "2014-07-18 15:53:15.589501", 
+ "modified": "2014-07-21 16:53:56.206169", 
  "modified_by": "Administrator", 
  "module": "Accounts", 
  "name": "Payment Reconciliation Payment", 
diff --git a/erpnext/accounts/utils.py b/erpnext/accounts/utils.py
index bc005d7..25a8adf 100644
--- a/erpnext/accounts/utils.py
+++ b/erpnext/accounts/utils.py
@@ -153,12 +153,12 @@
 		check if jv is submitted
 	"""
 	ret = frappe.db.sql("""
-		select t2.%(dr_or_cr)s from `tabJournal Voucher` t1, `tabJournal Voucher Detail` t2
-		where t1.name = t2.parent and t2.account = '%(account)s'
+		select t2.{dr_or_cr} from `tabJournal Voucher` t1, `tabJournal Voucher Detail` t2
+		where t1.name = t2.parent and t2.account = %(account)s
 		and ifnull(t2.against_voucher, '')=''
 		and ifnull(t2.against_invoice, '')='' and ifnull(t2.against_jv, '')=''
-		and t1.name = '%(voucher_no)s' and t2.name = '%(voucher_detail_no)s'
-		and t1.docstatus=1 """ % args)
+		and t1.name = %(voucher_no)s and t2.name = %(voucher_detail_no)s
+		and t1.docstatus=1 """.format(dr_or_cr = args.get("dr_or_cr")), args)
 
 	if not ret:
 		throw(_("""Payment Entry has been modified after you pulled it. Please pull it again."""))