I've ran into this as well. Certain override files or certain situations(such as using KSE to make your main PC a Jedi before Danooine) cause that to happen. Sometimes it is just simply saying the heck with it and erasing all your save games and starting over with no other saves.
I erased all my save files and removed an override file and then started over. The problem was solved.
Well. the best thing to do is just level up like normally and as soon as you get to Dantooine and become a Jedi is to use KSE to reduce your non-Jedi level down to 1. Don't remove it, since it does provide one advantage and makes certain skills: class skills.
Scoundrel(red)/Consular(green) is every skill is a class skill.