I think it's that ZoneAlarm doesn't remove the TrueVector service when it goes down, because if it was trying to modify the TCP/IP stack WFP (windows file protection, most notable in W2K and XP) would be all over it.
I was having the strangest problems where I could boot into windows but not access the internet, until I opened up ZoneAlarm.
My conclusion (possibly incorrect) was that the service worked fine without the GUI frontend (ZA), but would only allow programs through that you checked the "always allow" box on the ZA popup. With any other program, it would assume you clicked the "no" button on the popup and would not allow the program to access the network. Maybe removing the service/startup files would work, and it would save you from a rebuild.
To restore your TCP/IP stuff, if you're in W98 or Me, open up msconfig and there should be an option in there for "verify system files" or something like that (haven't run a 9x system for quite a while). It'll go through your windows files, and if it finds anything incorrect it'll reload the file from your Windows install CD.
Windows 2K or XP automatically do that verification (WFP) and won't bother you about it. You'll see entries in your event viewer if this is happening.