Usually these kinds of errors which appear suddenly and follow you around after uninstall involve something which isn't removed by an uninstall. After you uninstall you ought to clean the registry and remove any extraneous folders leftover. There are some good progs that can wipe out files that aren't useful. Also look at the order that you are installing things in. This problem was one I was having when I first installed SH3 with Grey Wolves. I can't recall how I fixed it but I think it involved how I installed mods.
It's the Game, then the patch (1.4b), then the mod then SH3 cmndr. However you said that it worked fine for a while. This would suggest something new on your computer altered something of how the game interacts with windows. So recall when the problems started and what new progs you had installed or if you had changed any major settings.
That's the best I can give you.
Cheers mate.
