Unfortunately, I think this has become a bit of a racket to sell updated versions of accounting software. I used to submit my VAT returns to HMRC direct from SAGE, but it stopped working a few months back (due to the MTB new rules) with a 'similarly vague' warning message displayed. The only way around it for me was to buy their updated software or submit all of the numbers on the HMRC website manually again.
My wife uses Xero and is MTB compliant, so far it is going well, but has also had teething problems.