Unfortunately I agree with you, the problem seems to be limited to some users so it follows it must be related to user configuration/environment. I was afraid it is the case from the beginning. I have been through this process a couple times to diagnose various issues and it is PIA. Oh well, what needs to be done needs to be done. Many plugins are self contained, or need to be called/activated to do something, prime suspects are obviously the "intrusive" ones like Pilot2ATC, TrafficGlobal, SAM and similar. I have already removed Data Ref Tool and Data Ref Editor, I use them in development of checklists and vrconfig files and forgot to move out. Sadly no difference.
I fly exclusively in VR, if done right the level of immersion is unparalleled. Highly recommended! BTW, I have checked in 2D too, same problem, so the missing overlay needles are not directly related to VR.
I will post when I find something - or if I cannot find anything.
Thanks!
Jarek