Sadly Rankor is correct, some mods don't do things cleanly. And I also agree that since he is making a big mod right now it's not a good idea to play with unknown mods (even though I would be happy to say ours is clean!)
I haven't played even my own mod for months during my current modding work.
Here's a good tip:
You can make re-installations very easy on yourself - make a fresh installation of Freelancer and then take a copy of it immediately (Select the folder in Explorer, Ctrl-C then Ctrl-V), and rename the copy as "Plain Freelancer Clean Copy" or whatever you will remember easily. If you have 2 or more disk partitions, save it on another partition (or another internal disk if you have one).
Then if you have problems all you need to do is delete the working Freelancer folder, delete the player accounts, copy the clean copy folder again, and rename the new copy to Freelancer. Then uninstall and re-install FLMM (FL Mod Manager), because it will not know that the Freelancer folder is not modded now. All of this takes me about 4 to 5 minutes instead of much longer, so it will no longer be too much of a pain.
If you settle on running 1 or 2 mods regularly then you can use this method to install a clean copy, install and activate copies with each of your mods (on the same disk as the first Freelancer installation), then you can switch between your mods by just renaming folders instead of activate/de-activate/re-install each time.
If you are interested, our mod is in test now, it's called RRJDS 2.81, and you can get it from our website
www.rrjds.com .
You can also get a feel for it by reading our players' activities and comments on our forums:
RRJDS Player Forums
It doesn't have problems with either FLMM nor with de-activation, but you should NOT use other mods or cheats with it because doing that will cause you problems.
We are also running TNG 2.76 on our main server so you can join us with either mod.
Roleplay: - the art of self-deceipt!