What about your accessories like rings and earrings?
Kronon wins this thread. Nothing is glitched, you are actually wearing heavily damaged ring(s) and/or accessories.
When you go to the repair NPC and click "repair all", rings and accessories apparently don't count as "all". To check gear durability, the easiest way I found is to look at the gear in the inventory tab, NOT under the gear and attributes tab. (Why would you ever check gear durability under the gear tab, that doesn't make any sense...)
If you scroll through your inventory to your currently equipped items, you'll see a number in the lower left corner that will be displayed as #####/#####. This is the durability of that item. Check the durability of your rings / accessories.
I haven't really looked into what processes or mats are required to repair jewelry, but at lowbie levels, I'd just as soon buy new ones before I waste my time figuring out how to repair. It's probably cheaper too.