Yes, I imagined the Linux <-> Windows thing would be a non-issue, just mentioned it for a shot at completeness.
No mods - pretty much fresh installations (no expansion at the time either - though I've since purchased it since I like the game so much)
Sorry for posting an issue that I can't further test at the moment (I hate it when people do exactly that to me), I just wanted to throw it out there and see if it rang any bells.
At such point as I can get together with my friend again and re-test I will document it better and try to grab some savefiles. (side note, will I need to disable my expansion to play with him now, since he hasnt purchased it yet?)