@Danest, It's most likely just that NMM is being stupid in some arcane way. The ESL limit is reportedly 300+ in the absolute worst-case scenario, up to 4000-odd if mods are sufficiently small. I haven't found anyone explaining why the limit works that way in detail yet, since I can't think of a reason why the ESL in slot FE000 is would affect the ESL in FE001, but that's what the documentation I've read says anyway.
One thought, do you have an ESP in slot FE/254? For some reason the game is happy to launch in cases like this, but I believe the ESP will win out where form ID overlap occurs. Obviously this will break your ESLs in strange, likely crashy ways. A well-written mod manager would prevent the use of slot FE when ESLs are active, or at least whine endlessly that you're going to have problems... you've probably already read my opinion on NMM, so I have zero expectation that NMM would catch this automatically.
What should I be using in place of NMM? I think I should have stuck with it, it was working except for a few esl. I think I've made a terrible mistake wasting a day on mod organizer. I can't run the creation kit through it, it just crashes... been googling all day for solutions. It looks like it's just broken and glitchy, so many other people having problems like this running programs through MO.