ATO have given me an extension until MYOB fix it but not looking forward to another 90 minute phone call tomorrow....
I have figured out a workaround but would rather not do it. That is if you tick the box below F1 and 'fill it in' but with no actual changes (as it thinks this box is ticked anyway).
So e.g. FBT Instalment is $3515 so...
-Tick vary instalment amount
-Estimated FBT for the year (F2) = $14060 which is 4 times our instalment
-Varied amount payable for the quarter (F3) = $3515 no actual change
-Reason code for variation (F4) = Code 31 although you can pick any code
Once I did this and clicked 'Prepare to lodge' it all worked. I would rather not do it like this however as we don't have any variation in our instalment amount!