Hrm…
Just a few more things:
1) Can you give a sample of how the permalink looks once you upload a document?
2) What version of WordPress are you running?
3) Do you have any extra information about the setup you’re running it on? (ie: Is it a shared host or VPS, what version of PHP are you running, etc)
Just need some more info because I haven’t been able to recreate this issue yet running WP 3.5.1 with WP Document Revisions 1.3.5. I’m trying to figure out what I need to do in order to trip this bug, so any extra information would help.