It's probably something I've mentioned in another thread, but last year MrsNWI and I had a situation where our DOBs were swapped somewhere between BA and AA, which impacted on our TSAPre being recognised.

As we'd had no issues with entering using Global Entry, it might suggest that the problem lay with how AA had interpreted the data feed. The AA agent at JFK Flagship check-in, after several minutes of furious typing, spotted the problem and corrected it.