Ok, I found the issue.
The subsite I am using on sharepoint was originally created as a meeting site. Meeting sites file saved documents in successive folders (1,2,3,etc), the all items view was displaying everytjhing in folder 1 but the submit buttin was saving things outside that folder.
When I changed the submit data connection to submit to /my library/1/ it worked fine.
That'll teach me to recycle someones old test site rather than create from new.