Hah. You know what? I might have to take back my earlier sentiments - maybe there is something specific to the launcher app or FSO causing this.
Don't burn me at the stake yet - I'm only changing my stance because I actually have something vaguely resembling tangible proof. Up until this point I've always had some kind of disc in my system's drives, but today ended up removing all that media. When I launched the game via launcher.exe, Windows suddenly (before the launcher even fully loaded) threw a generic "There is no disk in the drive. Please insert a disk into drive G:" (one of my DVD drives) with "fs2_open_3_6_12_RC4r_INF_SSE2.ex - No Disk" in the title bar. I repro'd the issue with Process Monitor running, looked for all instances of G:\, and found this:
Interesting, no? In a way this might also explain why another person was reporting the error didn't happen if they did their own build from source - seems like this might be a legacy of the configured dev environment from whoever built this particular exe, though I'm hardly a Visual Studio expert.
The error of course is otherwise utterly benign and I can skip it and launch the game with no impact - I expect putting a disc back in my drive will of course make it go away again too (the "not found" failure will occur gracefully rather than making Windows freak out about non-existent media). Just wanted to throw my two cents in here anyways that the problem might
have something to do with the way the latest builds were put together after all, since now there's actually something in the way of tangible evidence to present to this end.