One issue I've seen from time to time is how bringing up the GSX menu shows me the FI user interface/menu for a split second and then I'm returned to the v/c and the GSX menu pops up. What happens sometimes though is I don't get back to the v/c but for some reason my eyepoint/position has been moved from the v/c to somewhere at the cargo deck/department of the a/c This is in the PMDG NGX.
When this first happened I tried solving it by pressing the re-center key but to no avail. I then discovered looking at the P3D window on my 2D display what really happened is I was in some kind of an outside view rather than in the v/c view. Right-clicking in the P3D window on the 2D display and re-select Cockpit-Virtual Cockpit solved the problem and I was back in the v/c also in VR.
I'm not 100% certain but this might have to do with what shortcut you're using to bring up the GSX menu. I think the default one is CTRL-SHIFT-F12 or just CTRL-F12 if I recall correctly and after changing this to SHIFT-7 (after removing what was already assigned to that in P3D) the problem seems to have went away.
Have to do more testing though to know for sure but so far so good when I've been testing. Using this new shortcut, bringing up the GSX menu is much snappier.
Thought I would mention this for anyone else with the same problem and maybe also for the developers to look into. Not sure why the default shortcut for GSX would cause this issue when the same keys are not used elsewhere but this is what I've seen.