Nothing has changed and nothing has been fixed either. What you are looking at, it's just GSX closing the door as the last thing it does before departure, because it's assuming you forgot it so, it's not its normal automation.
After a certain update in the sim, when there's a Jetway, the simulator itself will close/open the door when the jetway extend or retracts. Now, fact it can't do it on the PMDG is not really relevant but, you think the "bug is back", but that's just because after this update, to prevent conflicts with the simulator own door opening, if there's a jetway, GSX will not operate the main exit anymore, and you noticed when GSX *does* operate the door when there's no jetway, it does it at the right time.
When there's a jetway, and you don't close the door yourself, GSX will make another last check during departure, to be sure all doors are closed, that's what you are seeing.
I guess it might be possible, for certain airplanes we know MSFS cannot control this way, we could make an exception and continue to operate the main exit (if MSFS could open the PMDG door, you might assume it was GSX...), even when there's a jetway. That's possible, but it's completely different than say the "bug came back".