I've found the cause of the dll-problem:
Due to that crash, FLMM somehow didn't deactivate the mod for 100%, and left my custom dll in the Freelancer folder.
So, when i activated the mod after that, I guess FLMM didn't recognize my custom dll as an extra dll, so no entry was written in freelancer.ini
I've deleted the custom dll after deactivating the mod, and now it all works fine again.
Sorry for the trouble! And thanks for the app that makes it all possible!