From MozillaZine Knowledge Base
- This article was written for Thunderbird but also applies to Mozilla Suite / SeaMonkey (though some menu sequences may differ).
New mail for a POP account is supposed to show up in the inbox. If it shows up in the trash folder:
- The most common cause is a inbox that needs to be compacted. Select the inbox folder and then use File -> Compact Folders to compact it. Its recommended that you move any messages you want to keep to other folders/child folders, and configure Thunderbird to automatically compact the folders to help prevent problems like this. See Keep it working and Compacting folders.
- A message filter might have moved it. Check the message filter log file.
- Check whether your junk mail controls are configured to delete junk messages rather than move them to the Junk folder.
- See if its due to the message being automatically forwarded. If the forwarding is due to webmail settings the message should not have been downloaded, so check whether you have an add-on that might do that. If you are unsure use "Help -> restart with add-ons disabled" to temporarily disable all add-ons and see if that has any effect. 
- The same problem can occur with IMAP accounts. If you also use a smart phone to read your mail check whether it might have deleted the message.
Message aging deletes message permanently, rather than moving them to the trash folder. So its not a possible culprit.