After updating to Firefox 3.6 (having xp professional) I have the same problems. But it only lasts for a few seconds and then I can restart Firefox again after this pop up you describe. Mostly it happens when I have to shut down Firefox after some website kind of freezes and wouldn´t allow me to close it. I think it has nothing to do with spy ware or virus, ´cause my computer is well protected.
Regards
SF