Which version of FLMM are you using? If you're using v1.1, downloading v1.2beta should fix some of your problems.
What do you mean about it not letting you deactivate mods? Doesn't selecting a mod and clicking "deactivate" do it? Also, "Tools\Restore Backups" will almost always fix any problems that come up, by restoring Freelancer to its original state.
The FAQ\Troubleshooting doc is for both; the questions cover common problems people come across (hence also naming it "Troubleshooting"
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Also, if you're having any other problems, let me know! I can't fix problems I don't know about
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