To diagnose problems with Thunderbird, try one of the following: *Restart Thunderbird with add-ons disabled (Thunderbird Safe Mode). On the Help menu, click on "Restart with Add-ons Disabled". If Thunderbird works like normal, there is an Add-on or Theme interfering with normal operations. You will need to re-enable add-ons one at a time until you locate the offender. *Restart the operating system in '''[http://en.wikipedia.org/wiki/Safe_mode safe mode with Networking]'''. This loads only the very basics needed to start your computer while enabling an Internet connection. Click on your operating system for instructions on how to start in safe mode: [http://windows.microsoft.com/en-us/windows-8/windows-startup-settings-including-safe-mode Windows 8], [http://windows.microsoft.com/en-us/windows/start-computer-safe-mode#start-computer-safe-mode=windows-7 Windows 7], [http://windows.microsoft.com/en-us/windows/start-computer-safe-mode#start-computer-safe-mode=windows-vista Windows Vista], [http://www.microsoft.com/resources/documentation/windows/xp/all/proddocs/en-us/boot_failsafe.mspx?mfr=true" Windows XP], [http://support.apple.com/kb/ht1564 OSX] ; If safe mode for the operating system fixes the issue, there's other software in your computer that's causing problems. Possibilities include but not limited to: AV scanning, virus/malware, background downloads such as program updates.

Right click the problem folder and select Properties. Then Repair Folder. Be prepared to lose some messages if the corruption is too bad. Then read this about maintaining your system to prevent corruption in the future, http://kb.mozillazine.org/Keep_it_working_(Thunderbird)

Try to rebuild the index file of the troubled folder. Right-click the folder - Properties - Repair Folder