Exactly, the systemwide availability link functionality at aa.com has been glitchy from the start, sometimes it's there sometimes it's not, etc. For future reference I would never rely soley on that for booking a flight. Call first, or at least put the flights you want on hold if possible then call to verify SWU space, etc.
Also, would be helpful to know the flights and exact EF search, many of us here would take a look and see if there might be something else going on.