Sorry for the cross post (to cosmo and LHC support), but it affected both for me, so I thought I'd mention it in both:
Just to confirm what I was seeing with LHC that broke all vbox apps... _something_ went wrong in LHC that left _something_ in ~/.config/VirtualBox on linux.
The result was even restarting the client, didn't clear it. The only thing that got vbox apps running again was to delete that directory. I have to assume there is an equivalent directory on windows hosts that could be causing some of the strange, system-wide (per user) problems with vbox.
The symptom ranged from the "Communication with VM Hypervisor failed" to randomly failing jobs "output file absent" and it also broke cosmo vboxes running on the same machine.
Got the X5690's up and running LHC. Running three ATLAS tasks simultaneously with no app_config. Downloaded Boinc+VirtualBox, installed it, fired it up and having zero issues.
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