I just upgraded ZA to 5.5 from 5.1. Settings are the same and preferences are set to load on startup.
Only problem is it doesn't load on startup. You have to open the program and it works fine from there.
I have checked startup at msconfig and it is checked off there.
What is curious though is that I have a file folder entitled Zone.com which has shortcuts to a list of games from Zone.com. Needless to say not related to Zone Alarm. Since upgrading that folder opens automatically everytime I restart the computer. Can't figure out how to stop that and wonder if they are related.