It's just the regular issue of mods being baked into GMM's backups
- Go to GMM/backups, delete both .bak files.
- .
- Steam users:
Steam -> Library -> right-click on FTL -> Properties -> Local Files -> Verify Integrity of Game Cache - DRM-free version users:
Reinstall FTL (remember to back up your profile!)
- Steam users:
- Launch GMM to create new backups
Mind you that if you've updated FTL to version 1.03.3, some of the total conversion mods may be broken (IS among them).