The first thing I encountered after downloading the retail game was that when I created a custom race I ran into a problem with the abilities selection. When I would "X" the boxes, they wouldnt stay "X"'d even when I had my full 10 points and I picked a skill that was only 1 point. (So it wasnt just that I didnt have the points.) After I restarted the game it went away, and I havent changed my custom race since so I dont know if it was just a weird, one time thing, or not.
Secondly...and this is a more troubling problem for me...My game plays fine when I first start it up. After a while, however, the game screen starts to flash and all I can see is the mouse cursor. It is especially bad when I try to create a ship and I stay on the creation screen for a while, or when I assault other planets. The battle screen has caused three crashes already, on top of crashing when I make ships and stay on that screen too long.
I am running an ATI Radeon 9800. I have 1gig RAM, a Pentium 4.
Most of the time the game runs fine, its just kind of annoying to have to restart the game after a couple of hours when the game crashes.