The upper pane shows that I have messages, but messages don't show in the lower pane.
The upper pane shows that I have messages in my Inbox, but when I click on one, nothing shows in the lower pane.
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It sounds like your mail file(s) are corrupted. First of all create a backup of your Thunderbird profile folder. http://kb.mozillazine.org/Thunderbird_:_FAQs_:_Backing_Up_and_Restoring
Then try to rebuild the index file of the troubled folder. Right-click the folder - Properties - Repair Folder
Note: depending on the corruption this may erase messages from the affected folder which cannot be recovered anymore. In that case you'd need to restore them from a recent backup done prior to the corruption.
Corruption is often caused by anti-virus software messing with Thunderbird mail files. It is therefore recommended to create an exception for the Thunderbird profile folder, so that the real-time scanner won't attempt to scan the profile with your mail.
For more information on the profile location see http://kb.mozillazine.org/Profile_folder_-_Thunderbird
Also see http://kb.mozillazine.org/Keep_it_working_-_Thunderbird