This looks like a married segment logic issue. This happens a lot with AA (and I suspect other carriers) and is not limited to upgrade and award inventory.

Various fare classes may be available for AAA-BBB or BBB-CCC when you look for AAA-BBB-CCC but not when you look for the segments individually. I've seen the reverse too where the inventory shows on one segment but not if that same segment is part of a multi-segment route.

When I set an alert on EF for an upgrade on a multi-segment route I set the alert using both the single segment that I am interested in and also for the entire multi-segment routing for which I am ticketed. If the alert triggers for just the single segment I call AA and ask for that single segment to be upgraded and I get it.

As hillrider said, this not an EF issue but the way AA makes the inventory available.