virtualbox.org

First time I've had any big problems after an upgrade, but today I upgraded to 4.0.8, and booted into my Vista VM. Everything looked fine, I got a notification about updated guest additions, so rebooted into safe-mode and installed them. After the guest additions installed I rebooted, and got a "this is not a genuine windows install"...so went through activation again, and it hung up.
I did a force reboot, and now after logging in windows just hangs at the Welcome indefinitely...rebooting results in hanging at the same place each time.

I can get back into safe mode, so ran "sfc /scannow", which identified some issues, but was unable to fix them. Checked the log, and the files it was not able to repair are directX related.

Coincidence or related to the experimental 3d drivers?

It's not caused by the 3D drivers, because I have two W7 VMs and one I updated gave the same "Not genuine" message. I ignored it, let it do it later and when I checked system properties, I got a nice message that Windows was still activated and genuine. A reboot after the GA update didn't give the message again.
So, with that experience, I'd say it's coincidence. And bad luck that your system got hosed like this. I hope you have a backup that you can restore.

Fortunately I back everything up regular, no data loss this time. I was curious if it could be replicated, so overwrote the machine with a backup and booted it up just fine, this time installing the guest additions outside of safe-mode with the 3d drivers disabled...same issue on reboot where activation is triggered.

So I overwrote it again with the backup and just haven't updated the guest additions again, it did trigger activation though, I'm still not sure why. For now I'll just leave it as-is with the old guest additions and try updating them later, maybe the activation just needed to finish before updating them.