I assume Firefox and the OS shut down normally, so database damage is not a potential explanation.

And that simply exiting and starting Firefox up again (without restarting the OS) doesn't cause this problem.

Do you have any privacy-protecting utility software that might be doing a privacy sweep at startup??

Did you check the permissions and owner of the Firefox profile folder (rwx) and all files (rw-) in it to make sure that you have write permission?