Edit 1: crap, the op actually ninja'd me. /fail
Couple things stand out. For one, you're running ExnemRuneSkulls w/out the corresponding FCOM plugin. You're also running OOO Level Stock and Oblivion Skill Rates at the same time. 1 leveling adjustment plugin per character

The obvious solution is to go back a few saves before you did the manual skill adjustments. If you'd rather not lose the progress, make a save w/ the aforementioned 2 mods disabled, then re-enable and try again.