I'm going to say it's not because of Module Inserter. The only way it could end up with even allowing 6 modules is if you had a mod installed that added these module slots, then configured ModuleInserter with them and afterwards removed the mod. I'll take a look what happens then tomorrow, but i doubt that is it, since you didn't use Module Inserter
I bookmarked the topic and will check what the devs say.