Yeah I'm finding this impossible to isolate as well (though it certainly happens often enough).  After
running Conkeror exclusively in safe-mode for a few days, though, I'm somewhat confident that the bug is
avoidable that way.

On the other hand, the only extension I have is AdBlock Plus, and the bug DOES persist if I disable that
in the extensions menu and run Conkeror normally.

Version:
conkeror.mozdev.org conkeror 0.9.4 (Debian-0.9.4-1)