I found a fix but sadly it deleted all my saves setup on profiles and set all my mod orders, and enabled/disabled mods to how they were when I first started so now I have to restart the game and spend another day fixing everything once more as if it wasn't a ***** the first time. This happened because the solution was only possible if I restarted everything. I ran into 2 seperate MO's, one of which knew all my changes and profiles and was a .zip, and the other was as if I never touched MO before in a folder, claiming it was the first time it started and did not have any of my MO progress. I used advise to run MO as admin (not sure why that never crossed my mind) on the MO that knows my progress, but I couldn't due to it still being inside a .zip. So my only choice in doing so was to extract the .zip into a folder and then run the modorganizer.exe as admin. When I did this, MO told me it was my first time I ran the program and had none of my progress whatsoever even though everything in the .zip that knew who I was and was extracted into it. As well even though the .zip still existed and seemed untouched, it lost all progress and was claiming it was my first time opening it, loosing my profiles and the saves and mod patterns with it. So restarting everything is no my only choice. Also when I said, "When I click Yes, normal Skyrim.exe starts instead of SKSE", I meant to say when SKSE started, it acted as if it was not SKSE and was the vanilla .exe causing all my mods requiring SKSE to deactivate, it also gave me some load errors, and messages saying, "SKSE is not running".