System crashes (not caused by Firefox) will cause Firefox to lose some settings and appear to be run for the first time.
History, Bookmarks, etc, seem to be fine.
Settings from about:config, Pinned sites on New Tab, and Bookmark bar, seem to be effected most times.
Sometimes, sites will not load again (no activity on the Network tab) until I clear the profile directory or go into Troubleshooting Mode once and come back.
I see that I can restore these by moving the contents of prefs-3.js to prefs.js in my profile's directory. Is there any reason why this isn't done automatically?
