KingofGnG: No, it isn't a game-related issue, is a Windows related issue. The Windows Registry stores settings for games, so the fact that the game "works" is only a matter of luck than functionality. And functionality should be preferred on luck. Windows is neither Linux nor Win 3.1 with their local "ini" files et all....
Of course it's actually Windows related with the registry settings and such, but often these settings are non-vital to the older windows games. There is some minor problems (like Diablo 2 autorun not being able to find the disc, but the game that has been copy pasted from some place finding the disc and playing without problem), but these settings depend on how the games utilizes the settings in Windows, and the configuration for the game at all.
All the games I mentioned are at least 6 years old and the only problem I've encountered with the games mentioned, was with Freelancer, which had a minor problem with the fonts, which I still played through the singleplayer camping on 8 times, made a save for every ship and explored every system in, despite that (needless to say, I didn't have much to do at that particular time).
I have never tested crap like this with newer games, because I cannot be arsed with the registry settings they depend on so dearly.