This happens to me once every 2-3 years for a month or so. I will not be on any upgrade lists or will be mysteriously passed over and end up #1 uncleared (friends/coworkers who are PLT etc. have cleared at T-48 but I won't and it will be full by airport control). After being frustrated for a month, it fixes itself.
Likely that the carrier pidgeon that AA uses pooped on the punch card machine.