JudasIscariot: I don't have all the info myself as I don't deal with the technical issues myself but it's probably the usual culprits i.e. weird graphic glitches (think rainbow colors) or framerate drops.
So, apparently it's a case of "rainbow colors". Apparently amd changed something in their drivers that broke 8 bit palette mode somehow.
If I remember correctly, SMAC is a weird GDI/ddraw hybrid thingy, so my ddhack approach won't work (at least directly).. I haven't tested it myself (yet), I guess I could dig up my SMAC cd's and install it on my wife's PC to see what the problem looks like first-hand..