I'm not sure if this is spicifically a firefox, or ubuntuzilla bug but I will give it a try here.
I updated firefox 3.5.7 to 3.6 (using gksudo firefox, etc) and restarted. As firefox started back up the "installing your updates" window started like normal but quickly stopped and displayed an error message "The update could not be installed. Please make sure there are no other copies of Firefox running on your computer, and then restart Firefox to try again." I checked for another running firefox process, but found none and even restarted my computer but I still get the same error message.
I checked in the /opt/firefox/updates/0/updates.log and found,
copy_file: failed to open or stat: -1,old-homepage-default.properties.moz-backup,2
so I tried,
cp old-homepage-default.properties old-homepage-default.properties.moz-backup
and started firefox but got the same error. I checked back in the log and found that ff found my copy but was missing instead,
copy_file: failed to open or stat: -1,icons/mozicon16.xpm.moz-backup,2
FINISH REMOVE icons/mozicon50.xpm
copy_file: failed to open or stat: -1,icons/mozicon50.xpm.moz-backup,2
So it seems to me that a bunch of files got removed and since firefox cant find them it won't update. Does anyone know what I should do?