Is this happening with Global Inbox or Unified Folders? For the latter, delete the smart mailboxes folder and virtualFolders.dat from the profile folder, with TB closed:

http://kb.mozillazine.org/Unified_Folders_not_working

This is a little beyond me:

    Use "Help -> Troubleshooting Information -> Open Folder" to display the contents of the profile using windows explorer (or whatever file manager you are using). Then exit Thunderbird and delete the "smart mailboxes" directory within the Mail directory. Start Thunderbird. 

'open folder option doesn't exist. where is the mail directory?

   If deleting "smart mailboxs" doesn't help exit Thunderbird and delete both "smart mailboxes" and the virtualfolders.dat file. That file is used for Saved Search (aka virtual folders) settings. A side effect is that if you had any saved searches they will be deleted and you will have to recreate them. The reason for deleting the file is Unified Folders is a "advanced folder view" that uses saved searches. Restart Thunderbird. 

I don't understand, I don't see any smart mailboxes. Virtualfolders.dat file?

Open the profile folder by clicking Open Folder in the attached picture. Close TB and delete virtualFolders.dat from the profile, then open the Mail subfolder and delete the smart mailboxes folder inside Mail.

Thank you for leading me by the hand on the file folders and data files. Worked like a charm and simple enough, just had to restore the columns I wanted in the folders.