Unassigned VAT and MTD filing

Last quarter I filed VAT via QBW Desktop and MTD for the first time. The amount due to HMRC was £5179.27. QBW zeroed the VAT Control account with a General Journal which posted the £5,750.00 of VAT owed and the £570.73 of VAT recovered. So far so good.

This quarter, the VAT Detail Report complains of that old horror, an Unassigned VAT amount,  in the sume of last quarter's VAT net payment, £5179.27. This is clearly generated by QBW's own automatic journal entry, so why it should be picked up in this fashion is a mystery. And of course worse, because the VAT100 now wants me to pay last quarter's payment over again, i.e. it reads:

VAT due                              £11,500.00
VAT reclaimed                    £ 1,126.13
Net VAT to pay                    £10,373.87
Unassigned VAT amounts -£ 5,179.27

The correct figures are:
VAT due                                  £5,750.00
VAT reclaimed                        £  555.40
Net VAT to pay                       £5,194.60
Unassigned VAT amounts    -£      0.00

Weirdly, if I proceed with the MTD filing, the VAT obligation is not the £10,373.87 shown on the VAT 100, but the correct amount of £5,194.60.

Is anyone familiar with this problem, why it exists at all after all these years of giving problems, why it hasn't been sorted in advance of MTD, and what is to be done about it before I file the return and potentially get into one of those pickles with HMRC?