Hi Wouter,
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.
Cheers,
James