GSX says "default jetways" and then nothing happens. Not with GSX, not with the ATC menu, not with the PMDG FMC ground services button.
That explains the question already:
- If a jetway doesn't work when called from the default ATC menu ( or any other way ), GSX won't change that, it will still not work.
- If a jetway works when called from the default ATC menu ( or any other way ), it will work in GSX exactly the same.
This because GSX doesn't do/change/alter anything in the way jetways work, they will still work (or not), exactly as they did before.
This, of course, assuming you are using it correctly, which means Disabling from the GSX Config Panel the GSX jetway replacement files for airports you have a 3rd party add-on. Normally, GSX will already do that automatically, when you install or when you update GSX. If you install a new scenery after you installed GSX and you are not running a GSX update check, you'll need to use the "Exclude 3rd party jetways" button in the GSX Config panel in the installer, to have GSX detect which airports you have an add-on for, and Disable its own replacement jetway files for those airports. If a scenery has a non-standard name (common for freeware), it won't be detected, so you'll have to add its code manually to the Disabled list.
The reason why you should NOT replace 3rd party jetways with GSX jetways, is because the jetway replacement files that comes with GSX are ONLY meant to be used with default airports. If you use them anyway, even if you might see the replacement jetways visually, they will likely won't work, because the parking names/numbers and position won't match (they are supposed to match the default airport), resulting in a conflict, that's why the GSX installer automatically Disables all 3rd party airports from jetway replacement.
If you are sure the jetway you are seeing are the ones that comes with the 3rd party scenery and not GSX ( which is the only correct way to use GSX on 3rd party airports ), the only possible reason why a jetway won't work, is because you parked in a position where the jetway cannot reach the airplane exit.
And THIS is the only place in which GSX is marginally related to 3rd party airports and jetways: if you followed the GSX Marshaller, the default Stop position it has calculated automatically ( lacking a custom specified one ), might not be the same as the parking position from which the original scenery developer tested its own jetway to work.
That's why it's possible to customize the GSX Stop position at every gate and, since that is relative to the airplane main exit, once is set and tested to work, it will likely work with any airplane. The manual explains this in more detail on Pages 41-42, the chapter named "Understanding the Stop Position"