I guess this could go on the upgrades aren't clearing thread, but it does seem conversion related. Today I had two flights that passed through my first (96 hour) upgrade window. The second had an upgrade sweep that acted as expected--R dropped from 9 to 3 and my upgrade cleared.

The first, however, did not. A reasonably full RJ with all signs suggesting an empty first class (F and A = 6, R=4, no seats taken on the seat map). No sign of any of that changing as the upgrade window should have passed. We're now at about T-88. I can think of three potential reasons. Either we are still experiencing the system not working because someone's ticket is out of sync. Or there really are times when R=4 is not sufficient. Or maybe there's an issue since this is a Shuttle America flight.