When you say you turned off all message filtering, you may not have turned off what's moving your messages.
There are different filters that are controlled in different places:
- Filters; these are controlled through
tools | message filters, and may include both filters provided by Mozilla, like SpamAssassin, and rules you create yourself.
- Junk Mail Filtering; with general options accessed through
Edit | Preferences | Security | Junk.
- Junk Mail filtering is turned on and off at the account level, accessed through
Edit | Account Settings then within each account
The junk mail filtering is a learning system, but it comes with some rudimentary rules built in as a start, and is turned on by default.
If you verify that all filtering is actually disabled, there are many other things that can cause this kind of symptom. There is a whole Mozilla Knowledge Base article on disappearing mail. Not all of the possibilities listed match your symptoms, but some of the possibilities include:
- corrupted index files (in your case, that would be a good bet, but there are other possibilities)
- anti-virus software deleting messages
- incoming messages sent with incorrect date
- messages read with a different email client
The solutions depend on the cause, and they're covered in that knowledge base article.