The "newer" version will be in C:\Games by default. I changed it in my installers, since a lot of people were having problems with their folder in C:\Program Files, since Vista's and 7's user account control often prevents programs in the Program Files folder to write into files, or the registry, which makes you unable to use setup.exe, or even the patcher!
Delete the one in C:\Program Files, it is definitely older, and it won't affect the other one in C:\Games.