A nice thunderbird article outlines some of the issues the user has had. These are good tips, since as he notes, thunderbird has some problems.

• Use compact folders routinely, it solves some glitches with how thunderbird handles email deletions. I haven't seen these issues but it's a good recommendation anyway. Global folder compact option is under: File
  
• "You can set Thunderbird 1.5 or higher, to first drop new messages into a temporary file before bringing them to the inbox. The command is Tools > Options > Privacy > Antivirus." Once there, check the "Allow anti-virus clients to quarantine individual incoming messages" box. I highly recommend this."
  
• If you open thunderbird one day and see no emails, this should solve the problem:
  << The first thing you should do is close Thunderbird and head to your Profile mail directory and sub-directories. Once there, delete all your ".msf" files. Then, restart Thunderbird. With luck, you'll be back in business. >>
  

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