That's strange... I don't know of any fix, other than re-equipping the armour. You could try using
iZakaroN's SaveEditor (or from
Kiya's site, with description) to remove the skill point you put into Repair, and see if the level from the armour bonus shows up properly after the save is loaded.
A fix would be best, but you really only need level 1 of Repair for the equipment you are using, since there are no penalties for doing your own repairs. I stored equipment with less than full durability, and once I had Repair to level 5 (including 2 rings with a Repair bonus) I would batch repair stuff to sell for the maximum amount (not that there is any shortage of gold in the game). Before that, I had plenty of broken stuff and equipment with full durability to trade with.