VAT problems. Please help

Hi, please can someone help me?

I have a VAT bill that both the HMRC and QB seem to think has been paid, but no money has ever left my account. 

I've phoned the HMRC and the woman on the phone was scratching her head wondering what had happened and told me to pay it manually, which I have done today.

The problem is that QB thinks that my VAT bank account is overdrawn by the exact amount that the VAT bill is for. This is impossible because my business bank account provider does not offer an overdraft facility.

I suspect that the problem stems from there being insufficient funds in the VAT account when HMRC attempted to take the payment - I should add that HMRC never raised any question about this and neither did I until now.

Of course I moved the right amount of money into the VAT account to make the payment today and QB then thought that my account balance was 0. I subsequently made the payment to HMRC and now QB again thinks I'm overdrawn by the exact value of the VAT bill. I would suspect that there is a doubled up transaction somewhere but I cant for the life of me figure out where it is.

Has anyone got any ideas or suffered this problem themselves?

Thanks in advance