How exactly are your skills lowered? Do you see this in your character sheet as an icon - "skill lowered"? If so, maybe you are wearing some equipment that lowers some of your skills.
Check you armor and shield.......Do they have an armor check penalty? If they do those will be applied to certain skills. I do not remember exactly which ones but a couple of the Rogue skills are effected (Move Silently, Hide, and probably a couple others.
Lowred Skills
Is that a bug or something?
Linear Mode
