I didn't see this one posted yet, so...
When I have the clipboard open I lose colors for the different countries. My country shows as black, everyone else as a dark gray. Sometimes minimizing the clipboard will bring the colors back for a short bit, sometimes moving the map inside the clipboard, sometimes they just come back on by themselves. They never stay for more than a couple of minutes though.
If I rotate my view so that a burning building is behind the clipboard the colors come back and stay. Finding a light-colored building and zooming in so it fills the display will also bring the colors back.
Specs are a T-60 Lenovo laptop, 2 GB ram, Windows XP SP3 will all patches, GMA 945 graphics with Lenovo's drivers (Intel's base drivers gripe and won't load), 1280x800 resolution. I have very little in the way of software loaded. AH2's graphics are set all the way down. FPS stays in the 25-30 range at all times though I do get a "stutter" while panning to the side. I have experimented with altering the colors of the enemies in the clipboard settings and altering transparencies but nothing has seemed to help.
Other than that the game is running well for me. My FPS is even a bit higher compared to lowest settings under the previous version.