sndwv: Reading through the comments on the nocd fix instructions on WC CIC it seems like in the current GOG-version the game always thinks disc 1 is inserted and no random side missions from disk 2 or 3 will ever pop-up, and the best you can get it (after hex-editing the exe) is the game to randomly offer missions from all 3 discs regardless of game progress, but there is no way as-of-yet to have them appear in their original 'somewhat but not quite random' pattern unless you have an unaltered movies.iff and edit cd.dat each time the game requires a disc switch.
Uhoh, that's not very good! Maybe someone should contact CIC and ask them if they had made any other progress in 'fixing' it since then?
I remember originally missing the fact that there were side missions, because the game is not very clear that there were different ones on different cds. The manual doesn't even discuss it, and you kinda have to just bumble your way into finding them on the planets.