forum_modules/exporter/exporter.py's export_upfiles() just creates an "upfiles" directory, which never gets populated with the uploaded files (at least in ZIP mode -- this seems to be the behavior of ZipFile). It shouldn't be hard to list and write the files over from forum/upfiles, so I'm planning to do that. Would you accept a patch to this effect?
I confirmed that the tar.gz export works fine. So, recursion is automatic for tarfile but not zipfile. I added a pull request #515 that fixes export_upfiles() in the ZIP case, via os.listdir. (Fixing export_skinsfolder for ZIP export would require os.walk, which I haven't done.)