This usually occurs because Thunderbird can not contact the mail server. Try rebooting your computer and observing for errors when Thunderbird tries to get your mail.

Have same problem, First it started moving important emails to Spam, Now those are closed. Spent hours trying to correct the problem and know of no other solution than to change business accounts (software licenses, etc.) to gmail or yahool. Have already gone to server and they said the problem was Thunderbird's not theirs.