The following is from HMRC Website :
From 1 April 2010 all cheque payments by post will be treated as being received by HM Revenue & Customs (HMRC) on the date when cleared funds reach HMRC’s bank account.
This means that you must allow enough time for the payment to reach HMRC and to clear into HMRC’s bank account no later than the due date shown on your VAT return. A cheque takes three bank working days to clear – excluding Saturdays, Sundays and bank holidays. This change does not affect any cheque payments made by Bank Giro.
If your cheque payment does not clear by the due date shown on your VAT return you may be liable to a surcharge for late payment.
HMRC recommends that you make your VAT payments electronically as this is safe and secure and, in most cases, gives you up to seven extra calendar days to pay or, if you pay by Direct Debit, at least ten extra calendar days. Please remember that if you file your VAT return online you must pay electronically.
Link to confirm :