If I am making a magic weapon, and I am a 10th level caster, how does the item special ability factor in?
Can a 10th level caster only make a +3 weapon? Or can a 10th level caster make a +3 frost weapon, or does that count as +4 even for the item creations rules?
This is really confusing I'm certain, but I am having a hard time asking this properly...
Yes you can make a +3 weapon, yes you can make a +3 frost weapon.
When you add a special ability to a weapon you use the higher CL (in this case either the CL for the +3 or the CL for the frost property)
In short, the limitation of 3*caster level is only for the magical enhancement (+1, +2, etc), not any additional abilities that 'cost' a +1 or +2 enhancement, like Frost and Bane and such.