I have a post on another skills issue here:
http://www.eqemulator.net/forums/showthread.php?t=24808
Basically, my issue isn't the same as yours, but I figured they are sort of related lol. My problem is player skills not being displayed properly for characters over level 70.
I think I found somewhere in the source that sets caps for almost all skills. Though, I think they are supposed to be set in the skillcaps table now. Maybe that is what causes the skill caps in red problems. I will try to see if I can find that part of the source again maybe tomorrow and post it here if someone hasn't resolved your issue by then.
I am no coder, but most of the stuff seems simple enough to find if you read through the source. I just have no idea how to fix things yet lol.