OCS doesn't handle this kind of situation particularly eloquently at the moment. We've been discussing on and off different ways of handling multi-file and interlinked submissions, but haven't come to any particular conclusion yet. Is there any chance you could send me a set of submission files that are emblematic of the submissions you get? You can email them to me at jmacgreg at gmail dot com. I probably won't be able to offer an immediate solution, but I'll be able to come up with a good bug report, which will be taken care of in due course.
There's also information on linking to other files in the system here
, although this means you'll have to edit the LateX file links.