It has happend to me many times. I have lost the bookmarks many times 
with Mozilla on the last years

It has happened with NetBSD 1.6.1_STABLE/Mozilla 1.4 and NetBSD 
1.6.2/Mozilla 1.7.3

I have installed NetBSD 1.6.1 on Laptop Dell Latitude (Pentium III 700)
The NetBSD 1.6.2 uses a K6-2 500Mhz Epox  motherboard.

I disabled soft-dependencies and the problems continues.

It is a problem that only affects to me or is it a problem with Mozilla 
or NetBSD?

I have lost the configuration of my old Gnome 1.4.x several times. It 
seems that the configuration files are truncated. (it is on my Laptop)

Two days ago I have lost the configuration of xfce4 (my K6-2 500) It 
seems to be the same problem.

I suppose that it happens (I am not sure), when mozilla, gnome crashes etc

I haven't lost a bookmark using Mozilla Windows for serveral years, and 
my cowerker using Mozilla on Linux says to me that he hasn't ever lost a
 bookmark.