First the bike has Mavic Cosmic rims; the problem is the rear derraileur will not drop down to the 12t. The derraileur is adjusted all the way out and still will not drop the gear down; so it is stuck at the 13t. Anybody have this problem, I think it is the Mavic freehub that is preventing it from working. The new parts are Dura Ace 10 speed.
The derailleur isn't supposed to make contact with the freehub, so your thought that the freehub is somehow preventing the derailleur from working doesn't make sense to me. I'm thinking that either your derailleur hanger is bent, or your outer limit screw needs adjusting.
Could be a cable problem. If the cable is disconnected will the derailleur swing over to the smallest cog? If not then the problem may be the high limit screw. Be sure to flip the small shift lever several times and take the slack out of the cable before re-attachingto the derailleur.