My one handed level is in red. In oblivion that meant you had a problem(disease, poison, etc) I went to a temple like in oblivion and had my afflictions banished but yet my ability stays in red. Any ideas or suggestions on what it could be?

Go to Magic > Active Effects.
There you can see any negative effects and what is causing them.

Possible the stat is damaged and not drained? Following Morrowind's logic if a stat is damaged it must be restored in addition to having the cause removed.