When I closed and reopened FSX, UT2 was there. I don't know if the missing UT2 had anything to do with GSX fully working at the arrival airport.
That's possible, and it fits in my theory of a generic "Simconnect clobbered" issue. Regardless who's causing it, it's possible that, when there are many 3rd party modules, all communicating with FSX using Simconnect, if the communication channel becomes too crowded, the sim might not be able to process all requests, and will start skipping some of them.
For example, GSX might ask to create a vehicle, and the request might be ignored, because the sim was too busy processing other requests from other addons.
As with ASN, if UT2 was unable to create an AI plane, you would hardly notice it, but since GSX is supposed to create objects all around your plane, a problem like this cannot be missed, so it would seems like a GSX problem, but in fact it's just Simconnect too taxed by too many installed addons that it cannot work correctly anymore.
I'd try with disabling every 3rd party addon and leave just our two modules ( bglmanx.dll in the DLL.XML and couatl.exe in the EXE.XML ) and see if this will fix the issue definitely. At least to confirm this is the problem.