Input lag when BeamNG is in foreground

I'm currently facing a problem with gamecontroller Input. I'm using an XBox controller to play the game.
For some reason, if I have the game in focus, the game will start to lag behind the inputs. At the start of a session the inputs work normally, but after 30sec to 1 minute, the input starts to desyncronise. After about one to two minutes of playing, the inputs will lack behind about 10 seconds. This only happens with the input from the gamepad, not the keyboard and mouse input.
But if I put the game out of focus, the inputs will be received correctly and no lag will occur.
I have tried other games, but in none of them I could reproduce this behavior, so it seems to be an issue with BeamNG.
Does anybody has an idea what could cause this?

System specs:
- OS: Windows 10, Build1607
- CPU: Intel Core I5-4690K
- GPU: AMD R9 290

 

Yes(ish)
I've recently moved my Windows-stuff into a qemu-VM (with PCI passthrought for the GPU). On the normal System everything works normally, inside the VM there is input lag.
I have also tried forwarding a PCI-USB-Card into the VM with no change
(I think this is whats considered to be an "edge case" )