With mozilla-0.9.9 in beta3, bookmarks added during a mozilla session are only permanently added if mozilla is exited cleanly (File -> Quit). Things like crashes, or logging out of X (which results in exiting Mozilla via pkill -15) lose all bookmarks which were added during that session. Presumably, bookmarks are no longer flushed to disk as they are added. Instead, they only get written when the browser exits. Tailing ~/.mozilla/default/mumble/bookmarks.html confirms this as well. This has caused me to lose lots of bookmarks, until I figured out what was happening. The old behavior of netscape and prior mozilla releases was much more user-friendly.
Still true with beta4
7.3 gold fixes this