ok, sweet thanks for this, ill give it a go, MSFS just seems to be a pain in the ■■■ to get working for VR for me so if i only have to do something once per flight then its fine
unfortunately it didnt stay, i still had to press CTRL+0 a lot. idk why. 
The two of us can’t be the only ones with this issue. Mine is almost identical to yours. Only happens in VR. No change to hardware configuration, usb ports/hubs, etc. from SU6 to SU7. Every controller except my pitch/roll (TM TCA Airbus) stops working. It seems to coincide with the mouse almost ‘losing focus’ on the app. Most times, a middle click of the mouse enables the mouse cursor again and snaps all the other controls back to normal operation, but other times, i have to keep moving the mouse cursor (to prevent it from timing out and going invisible) in order to make throttle adjustments, etc. I have tried everything i could think of to fix this, including usb power management settings, tweaking which USB ports I’m using, setting my mouse/controller settings to default and I’m at a loss. Rolling cache is disabled. Again, only happens in MSFS. X-Plane, DCS in VR are working without any issues. I’m not sure if it is linked to any of the following other various issues we’re having, but it seems to me that there are a number of underlying issues with controls in general that are plaguing SU7:
https://forums.flightsimulator.com/t/toolbar-broken-in-vr/472150/340
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It’s not just the two of you. I’m having severe issues with HOTAS controls in VR, and it’s completely ruined the game for me. It started with game of the year edition.
For VR I’m using an Oculus Rift CV1 with Oculus Touch controllers. Controller is Thrustmaster TCA Airbust joystick & throttle quadrant. Here’s what I’m seeing:
- If VR touch controls are enabled, my HOTAS does not work. At all. Since I don’t see any way to disable these in game, I have to pull the batteries out of the Oculus Touch controllers.
- Once I’m flying in cockpit mode, buttons on my HOTAS randomly stop functioning. Some axes will also randomly stop functioning. Most frequently it’s the rudder, but sometimes it’s one or both throttles, and once or twice the elevators and ailerons have stopped. Going into the control settings and backing out restores operation… for a minute or two.
- Here’s the crazy part: If I go to external camera - the controls work perfectly fine. If I return to internal camera, they’re still busted.
None of this ever happens if I’m not in VR. In VR, it’s constant.
My hunch is the VR controller support they added recently screwed things up. But I can’t play the game until this gets fixed. Frustrating.
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I’m having the same issue. Using the t.16000 FCS and it keeps losing my throttle controller in VR. No issue in 2d. Going into and out of control options fixes it, for a bit…
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It seems to be fixed now. I set msfs to run windowed with a lower resolution. I also updated to the newest Nvidia driver, 497.29.
Run the menus in 2d mode using oculus link and then after clicking fly now, switch into vr. Still need to use tab to bring up menu bar and ctrl+0 to get the mouse to interact with the windows.
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This appears to be the bug, here, if anyone following this thread hasn’t seen it:
Be careful not to drag your mouse over any overlay windows as a temporary work around.
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Hurrah (sort of) this isn’t just me! Joystick never drops out. Throttle and rudder do. A quick wiggle of the mouse and as you say, everything comes to life again. I’ve only tried this in VR as quite frankly if I have to run MSFS in pancake I’ll be flying any other sim in VR first. 
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One thing I think might have helped me that I changed recently is to set the Assistance → User Experience → AI Piloting in Cursor Mode to OFF. My controls don’t seem to be dropping out as much or at least they seem to be coming back. Worth a shot for anyone having these issues.
Besides not hovering your mouse over a window has anyone found a solid solution for this? I posted to the MSFS zendesk and am awaiting a response. I have the exact same issue you guys are dealing with.
The people reporting here that the issues are software related, not (USB) hardware related are correct IMHO. I am relatively new to MSFS, but have a full motion driving sim rig and decided to add a Warthog HOTAS to it and start exploring flight simulation. I mapped left/right rudder axis control to my sim clutch and accelerator pedals, and in 2d triple screen format, it all works perfectly. After doing the first 8 or 9 training exercises, I thought I would try out my HP Reverb G2 headset and initially was thrilled with the results until I realised my rudder control had stopped working. I also noticed in one exercise that throttle was not working, although the cockpit graphics showed the throttle know moving in and out (but no actual engine response strangely). Rudder control immediately returned in 2d screen mode.
Initially, like many suggestions here, I suspected USB conflicts (I have a lot of USB devices connected from this rig). But swapping out ports and disabling devices changed nothing. I then tried remapping rudder control to the keyboard and it still became disabled in VR mode.
Today, though, I discovered the following… the pop-up dialog with instructions from the Flight Instructor is displayed in the direct centre of vision at the beginning of an exercise. This is truly annoying as it generally blocks the view of take-off/landing approach, so I would always move the message box to one side with my mouse. For a change, I decided to close it by clicking the little X in the upper right corner. Rudder control immediately became active. As soon as another message box of instructions popped up, rudder control disappeared again. As soon as I closed it, rudder control returned. So there is a definite software problem in VR mode. It’s fine to try and close messages every now and again, but theres inevitably a message displayed right on approach before flaring and you just don’t have time to dismiss the message before you’re on the tarmac and veering out of control off the runway without rudder control.
Being new to this forum and MSFS in general, I’m not sure if theres a better work around, or a setting I could change to address it, and I dont know how I go about reporting this bug. Maybe some of you here know what I should do with this information??? Cheers