@emoKittenCZ
There are too many people here who automatically go attacking EA for everything wrong in this collection pack. And while the pack indeed has a bunch of problems, this particular problem is not due to the repacking in this collection, and has nothing to do with multi-core CPUs, so it's only fair to point that out.
It really is completely Westwood's responsibility for using undocumented and unsupported functionality in the old DirectDraw system instead of following the official specs. In this case, if I remember correctly, that unsupported feature was giving the colour palette to DirectDraw just once at the start and then just assuming it would remember it indefinitely for all the following graphics redraws, instead of specifically setting it again each time. It's entirely possible that even in Win95 it was possible to corrupt the colours in the game this way if you alt-tabbed out and did some other stuff that happened to use that same DirectDraw system.
I've seen Westwood's coding when I dug into these games. Trust me, while the results are undeniably awesome, there's plenty of weird and awful shortcuts under the hood.