I had a similar experience except only my shared directory was wiped and when my firewall froze. Maybe stupidly, I CTRL ALT DEL'd before restarting the computer leaving the system open.

In that short time, something deleted ~1200 files from the shared directory. I think the alert that was around that time was 217.36.8.57 (UDP Port 1025) but not absolutely sure. Don't know who it was - don't have the pro version of the firewall.

Luckily I have a backup, but has anyone else seen this type of file loss?