I ran into a similar problem installing a game. I installed it, then ran into an error while files were being copied. When it crashed, I coudln't uninstall the program and couldn't get a second install to work. Ultimately, I removed my windows partition, recreated it, and reinstalled windows. This time, I installed every windows update I could get my hands on. (Which means selecting "custom" from the updates page, installing everything, rebooting, doing it again, etc.) Then I went a little further and (because it was a game) installed directx.
This time around, everything is much more solid. Programs like Trillian still give me a problem or two, but everything else works as it should.
Mark