I had a similar issue with booking a codeshare where the operating carrier was BA. I believe the issue was to do with a 5 minute difference in the departing flight times between the BA operated flight and the AA code share. Now, that said, when I rang AA to see if they could book it for me they couldn't get the same price that their site and Matrix were showing so that does give credence to the phantom availability argument. In the end I ended up booking a different combination of flights that avoided using a codeshare but I had to switch the POS to UK instead of US.