Sorted! Go into Change User on File VAT MTD & remove the authority to interact with HMCE (this takes you into Gateway). Then need to go back in & authorise again. This worked for us but took a while. Needed to click File VAT MTD button several times, may just need a little time. 

I have 3 companies & the fix worked on all of them. Just hope it doesn't reoccur!

Hope this helps anyone else with same problem