The integration with Kashflow (and especially the re-integration after the initial one) almost never works well. It is confusing the clients when they have to click reset of the API Key, when should they click Update, and the way it works seems to be very precise and returns an error most of the times. Kashflow is the only accounting software that returns such issues so surely this can be made easier and more simple for the users. Your time is greatly appreciated, thanks!
I was able to fully integrate with AccountsPortal https://www.accountsportal.com to MTD. Easy to submit my VAT returns directly to HMRC. How long have you been having the problem for?