I've had this issue many times with various versions of ZoneAlarm, but I've never had to re-boot. If I understand correctly what you are saying it's just ZoneAlarm that's frozen not the whole PC. When this happens to me, while making changes in Program Control, I just log off my windows user and then log back on again, clicking the "end now" dialog that comes up for the open ZoneAlarm window.

When this does happen it's very intermittent and it's never really bothered me enough to be worth posting anything about; and I guess I've just got used to logging off and then back on again when it happens.