I guess that because our eq client is not a classic one, it lets us skill up past classic cap per level, but the server keeps us at classic cap ... more or less
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Since our skills (on client side) are higher than what they should, they are displayed in red and capped according to the server.
Kinda like if you deleveled your character.
Everything regarding a particular skill will be based on your server-capped skill value (the one displayed in red in your skill window), but if you go to your trainer you will see you client-capped skill level (maybe because no server check on trainer window).