Same thing happened to me two days ago, I was playing a game that crashed, had to reboot and when my PC came back it was like I had just installed Sygate fresh, it was asking me for permission for websites and Instant Messenger and stuff. I had to basically reconfigure my firewall all over again.

It's worth noting however, that all of my Advanced rules were still in place. Doesn't seem to harmful, although it's an example of my computer exhibiting a little more personality than I'm comfortable with.