I'm starting to run out of ideas. Just a notion: try launching Netscape, changing some setting that will be written back to prefs.js, and checking the time stamp on the prefs.js file before and after.
For ease of discussion let's say the main Navigator preferences pane, in the "Select the buttons you want to see in the toolbars" section, check (or uncheck) the "Go" checkbox. This I think is an innocuous pref, definitely stored in prefs.js. Quit Netscape to be sure it has tried to flush the prefs to disk.
Does the timestamp on the file indicate that it's been touched? Is the setting still not remembered? We're investigating two things here: whether the prefs file is being touched at all, and if so, whether innocuous, simple settings that probably wouldn't interest even something as potentially nosy as Norton Systemworks are being interfered with.
If the file and its parent directory are writeable I expect the timestamp to change. If the timestamp doesn't change on a writeable file then something must be wrong with Netscape but I've never seen Netscape fail even to try to save the file. If the timestamp changes then I want to think Netscape in general is trying to save prefs changes but is being prevented. If this innocuous pref change, unlike other settings, is
not lost, things just get more interesting.
Another thing you may want to try, change the "Go" pref yourself by hand. (With Netscape not running, use Notepad to) add this line to prefs.js, anywhere:
user_pref("browser.toolbars.showbutton.go", true);
Save the file, launch Netscape. The Go box had better be checked.
UserAgent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.7.3) Gecko/20040928 Firefox/0.10
