It's just the regular issue of mods being baked into GMM's backups...
Go to GMM/backups, delete both .bak files.
Steam -> Library -> right-click on FTL -> Properties -> Local Files -> Verify Integrity of Game Cache
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).
So perfect! I'd kinda sorta seen this suggestion around here, but thank you for a succinct and clear explanation! And thank you as well speedoflight, I was indeed using 1.4 at first, but another very helpful community member got me a link I could use for 1.7