You need to go into Sage 50, open the VAT Return and "tick" the box for "Submitted" manually. It won't automatically do it for you when you use the module. It only does it for you when you use Sage 50cloud and do the return via Sage 50.

Thanks Ian, I've checked this box in Sage Accounts and it's showing as submitted now. 

This is contrary to the instructions in your knowledge base article which seems to suggest after processing using the MTD module "In Sage 50 Accounts, the VAT Return now shows a status of Submitted".

Thank you for your help though, I just wanted to check something hadn't processed correctly on my system.