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The most likely thing is you didn't check the boxes correctly, or loaded it incorrectly. I recommend doing the hack again, because its hard to fix your problem with limited information on the problem from you.

The CVAR tool edits values once a mission has started.. So it "remembers" these values until you quit that mission.. Some CVARs can be kept active, other reset automatically when you start a new mission (just like in Spec Ops) & you're gonna have 2 do that everytime, cause there's no option to save in a spec ops mission.. I never had anything else in spec ops than lasersight & superjump..