Thank you, Emma, i was hoping a backup/restore would be the last resort.. you know what us system admins are like!
The assignment is not being created by duplication, just to add.
I'm fairly confident the permissions for the course and the assignment are correct. I've spent a lot of time looking at this course and comparing it to a neighbouring course (in the same category) that works flawlessly.
We'll give a restore a try and see what we get.