Mine changes the sim.cfg file, but i was very careful about, and deliberatly avoided messing with the wave mech settings
edit:
It just occured to me hes running my mod (which ramps up the AI), and another AI difficulty mod at the same time. There has to be a mod conflict there. If you run FTT, you really dont need to improve the AI. That is, unless you want it even harder then what ive set it at.