I purchased GSX a week ago and had similar issues in VR. I got up to speed on some of these threads as I sought to reproduce the issue, and here are my in-progress thoughts.
First, I would agree with the thinking that it is not just GSX but rather numerous addons causing the issue. If I link just the GSX mod and lose all else but a few 3rd party aircraft, the panels in VR operate as expected. If I introduce more addons but not the FSLTL traffic injector, eventually things will start misbehaving a bit. For instance, hitting ESC a few times won't bring up the MSFS menu, there will be a glitch window refresh or artifact and then suddenly the menu will appear. If I fire up the sim with everything including the FSLTL injector, it almost always glitches fully with no ability to get windows back.
Another reason for my thinking that the issue is not just with the GSX addon is that the bugs can start to impact non-panel related items. For instance, in the Aerosoft CRJ, my whole plane will be malfunctioning when the panels are bugging out. Sometimes the EFB iPad won't be clickable and the battery switch for the plane won't bring it to life. Or clicking on the door icon on the EFB iPad will open the door but the label on the GUI will continue to say "Closed" rather than "Open (Stairs)" or something. Basically the wheels seem to fall off on other parts of the sim which would make sense if some simObject threshold was being hit. And this happens more readily with my Aerosoft CRJ than with something like the default Cessna 152, which seems to support it being some threshold being hit.
What I did find is that I can seem to launch into the sim running GSX with FTLSL installed and if I hold on running the injector until everything is loaded and working properly, I can then run the injector a few minutes after the sim comes up and it seems to be fine, even with continued entering/leaving VRs. I need to test this on a longer flight, but it seemed to do the trick.
My last note is that the comment about the sim hanging by Markymarksti is something I am experiencing too. When the bug manifests, if you CTRL-Tab back into monitor-mode and quit the flight, the sim will almost always fail to exit the flight for me without my force-killing the sim. I have left it up for an hour and the progress bar gap just gets smaller and smaller without ever completing. This makes debugging it or even coping with it extremely painful because restarts are costly. You can't just quit, kill FTLSL, and re-enter. And, in case this helps with debugging, what is strange is that every time I kill it during one of these hangs, when I try to relaunch the sim, it will always complain that the simulator is already running and, sure enough, that will be the case. I can always find a duplicate or new FlightSimulator.exe process. I am not sure what is going on with that. It feels to me like a 2nd process is getting spun up on my closing the original window. Its strange. I can kill it and I will see a new process start up. I'll try to debug this more in case it gives some insight into what is going wrong.
I will continue to debug this and see if I can narrow down possible configurations or solutions.