Windows 7 startup repair deleting my game?

I just installed rise and fall civillizations at war, which in order to install I had to copy files onto the harddrive from my disks. Right after it installed fine it said it needed to install additional libraries (which is normal for this game) along with a needed reboot (also normal) after the reboot windows startup repair pops up, takes forever, and deletes my game. How can I fix this? (And I can't get around the repair, cancelling early makes u restart and cancelling aftr a couple minutes cause it to say it cannot be cancelled)