This is the second time i had this problem, the first time was with Mount and Blade Bannerlord the second with Skyrim AE at some point in the last few months i had both games installed modded and runing, but my main HD is a small one so i can only have 1 game installed at a time, had modded bannerlord worked fine then i installed skyrim modded worked fine, then a few days ago i re installed bannerlord and base game worked fine but mods just wont launch, after that uninstalled bannerlord and installed skyrim same thing happens but when i open console to check the SKSE version its shows me the correct one but when i load a save or start a new one mods just wont launch, MCM doesnt even appear in the game settings menu.
one more thing if i move the games to the backup harddrive that is much slower and i only use it for storage the mods work but the load times is skyrim to up to 6 minutes per load screeen