First off, are these multi-classed characters, or dual-classed (human)? There is a difference, in that dual-classes are formed after the character has been made, and when you choose a second profession, the original skills become unuseable until you reach an equal level in the new profession. Now, if you started them off with two skills (non-human), then the problem is simply that your gear is restricting your abilities. Cleric/Mages can only cast Mage spells with no armor on, like normal, and Thieves need to be wearing Studded Leather or less, or a set of Elven Chainmail, no matter if they are multiclassed or not. That should take care of any problems you have.
-Wrath
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