Windows folder completely wiped ?

I've been experiencing some issues with Windows over the past few years but this one is well over the top. I switched my home computer on today and I got no response at all, it wouldn't boot from my primary windows setup. I happen to have another setup on a secondary drive just in case something like this would happen so I booted from that only to find out that my primary windows folder of the first setup was completely empty.
If anyone has any suggestions on how something like this could happen please post a comment. I have Kerio Personal firewall and AVG antivirus on that machine so an Internet attack seems less likely than possible.
I am as confused as I could ever be on how something like could happen..