Denatured alcohol is better than isopropyl. You sure don't want to use rubbing alcohol! It's got oil in it.

I've heard the same about acetone, that it'll eat up carbon arrows. I don't know if there's any truth to it. I wouldn't soak them overnight in the stuff, but I don't see how a wipedown with acetone will affect them in any way.

If you're really having problems with glue sticking, then try cleaning the shafts off and letting them dry overnight before fletching. That way you'll be sure that all the solvent has evaporated out of the carbon's pores.