2007/08 tax return out of time or not?

I realise that this area has been covered here before, but this situation is slightly different.

HMRC issued 2007/08 return in June 2012. Tax return submitted within 3 months of the issue date. It shows a repayment due. HMRC decline to process the return and so deny the client the repayment. HMRC quote the 4 year deadline for the return as running out on 5.4.12. However, isn’t the deadline the later of 5.4.12 or 3 months after the issue date of the return?