This could be a complete shot in the dark but I used to use the free version of zone alarm and never had any issues, then I upgrade to the pro version and all of a sudden my computer would freeze, take 20 minutes to boot, etc. There was an issue with the service it runs to scan packets I believe, it's been a little while though. As soon as I removed ZA and installed another software firewall I never had the trouble again. Unfortunately I never figured out what caused the problem, but I knew it was the ZA service because when I kept it from starting but let everything else run, crippling the firewall but letting it's front end run, the problem suddenly went away.

Maybe it was because part of the upgrade went wrong, I don't know but you might want to try using a simple free one, if you don't have a router/hardware firewall in place, and seeing how that works for you.