Let me first say that Windows Repair is fantastic. I recently cleaned up a ZeroAccess variant on my machine, and it was the only thing that got the Firewall, Defender, and Update going. Truly Awesome Work!!! I'll soon be using it on another machine at our home as well, if needed.
I found that after I had applied the repairs in WR, VirtualBox would not start, saying "Failed to create the VirtualBox COM object". Fortunately, I backed up my registry and did a system restore point, as prompted by the program. Looking at the technical support on that issue accomplished nothing. Uninstalling VB and reinstalling would not make the problem go away. I restored the registry, and it went away.
I then proceeded to apply the fixes a few at a time, instead of applying the defaults. I had applied a lot of them, and got most of the non-working services working again, working from the top down; except skipping ones that likely wouldn't be involved. I got to the item "Repair Proxy Settings"; and remembering that VB installed network adapters to allow the virtual machine to communicate with the outside world, I skipped it, in favor of "Restore Important Windows Services". This finally had Windows Firewall, Defender, and Update working; AND VB working at the same time. Whew! That had been an involved cleanup.
Thus, I think "Repair Proxy Settings" makes VB irreparably broken. It might be another default setting; but I think it's probably that one. Ones it certainly is not, are the ones I used the second time around:
Windows Firewall
Windows Update
Remove Policies Set By Infections
Register System Files
WMI
Winsock & DNS Cache
Restore Important Windows Services
Other ones that don't cause the problem are the ones that are not enabled by default - or at least I'm pretty sure they don't.
I'd fool around with it more and see what the problem is, but after that lengthy malware cleanup, I'm spent. I suspect you'll be able to reproduce the problem; but if not, post here and I can try to narrow it down eventually. I'm just trying to pay it forward, so we can have the tool that M$ should have made in the beginning, a repair function for Win7, even better. Keep up the good work :P