OK, well I can only guess your install is still bad, or something on your machine is interfering with the installation process (such as an anti-virus app). I'd move your saves elsewhere, uninstall again, delete everything as before. Also delete your GG installer, and download that again. Install again to a new directory, apply the 1.03 patch and hope for the best!
If it still goes wrong, I'd think about moving to a different machine or moving your machine to a different location, to see if there are still problems like this.