In addition to what njvandy mentioned above its also important to note that BXP/SWU/miles upgrades come from a different inventory (C) than normal domestic comp upgrades (R).

In theory AA should release C space before R, although this doesn't always happen. Especially on a normal domestic flight like LAX-ORD, you could have a GA that doesn't want to mess with clearing any upgrade certs (whether BE or miles etc.) and just releases all remaining upgrade seats to R to be done with it.

BE upgrades are one of the last good uses of BE points, however I never attempt to use them unless the upgrade can be confirmed at booking or sometime before the flight.