Originally Posted by
TakingMyTime
Check your pads for anything they might have been picked up and that are stuck in the pad. For some reason my Bontrager rims that came stock with my FX seem to shed small metal shards from the rim to the pad. I can tell because every so often I'll get a metal on metal sounds from the brakes. A pair of tweezers or small blade usually does the trick removing them.
I recommend changing pads -- it's likely the pads and not the rims themselves. The Bontrager AT-750 rims seemed to shed a lot of aluminum bits into the stock Tektro pads, but dual compound Kool Stop pads cured that immediately.