X-COM: Enemy Unknown (2xDVD9 to 3xDVD5) *INNO SETUP*

[pakrat2k2]

see where it says

#define ProgramFiles "E:\Program Files (x86)\2K Games\XCOM Enemy Unkown"

that doesnt speciy anything other then MAIN gamefolder so inno will compress whatever subfolders are beneath that inputted game folder. It WILL be all compressed regardless if there's 1 subfolder or 100 subfolders. The only thing that should NOT be there is the original uninstall files, just move them out before compressing.