As from your original post, you were using Webtop at that moment and all in a sudden with the HDMI cable unplugged, then the phone rebooted.
At least a panic log is needed to verify whether this is related to Nebtop, or the stock ROM+Webtop.
As Nebtop has no listening of the HDMI cable plugging/unplugging event, it should had done nothing at that moment.
And your current state sounds like the file system is corrupted. If I have no way to fix this, I would try to backup the current state first, then try to revert to the stock. (not sure if Atrix 2 has any stock image leaked )
Finally, I'd like to help to identify the actual cause of the reboot, only if you could look up the kernel panic log at this location /data/dontpanic/apanic_console (this is the path for one of the Motorola phone, it could be changed for Atrix 2).
Just a word of warning:
This app totally screwed up my phone. I installed it and was using it just fine for a couple of hours. Then all of a sudden, the phone becomes unresponsive. I unplugged the HDMI cable, and it rebooted. I didn't think anything of this. Just found it a little odd. Since then, any time I reboot the phone, it is reverted to the same state it was in right before the crash. The text message I had not yet read is re-received as new. All app updates are reverted. All new apps aren't installed. All new texts (since then) are gone. Apps are force-closing left and right. Be VERY careful with this app. I'm not sure it's really ready for prime-time, even now.