SH3 commander problems

[flakmonkey]

this only applies if your using vista, but its sounds like you went and did something silly like installing sh3 into the program files folder! (good old windows eh, have a folder called program files and make it break any programs you put in it!)
The folder permissions in vista may be preventing sh3 commander from actually altering any of the game files.
If this is the case the best solution would be to re-install sh3 outside the program files folder, or alternativly set sh3 commander to run as administrator.