Yeah, it replaces all of them. Except the shadow evo troopers, I'm not done with them yet, but I'm getting there.
Slinky, does it actually not let the program run, or are you simply afraid to run it in case the warning is right? It should be safe, but most anti-virus programs detect a false positive because of the way it basically hijacks exe files and modifies the files they load, which is similar to what real threats often do. If it's actually preventing you from running it, I think there's a way to disable the warnings for individual programs, but I'm not sure how.