I recently upgraded from Mozilla Thunderbird 2 to the new Thunderbird 3 release. For a few days everything was working fine with the new default settings. I have a few email accounts which Thunderbird fetches mail for and I didn't want to use the new Smart Folder mode. So I changed back to not using it. Everything appeared ok, until the next day. I returned home from work to find no new email. This is highly unusual as there is usually some for of advert for an online store showing me the latest offers, especially around christmas time. This lack of email continued for a few days, to begin with I attributed this to my ISP who were reporting problems with the email system. Today after 4 days with no new mail it was time to explore more options within Thunderbird and try to find a solution to the problem.
The solution came about by chance whilst browsing the Account Settings screen. The route to the solution from the main screen is shown below.
Tools > Account Settings > Click 'Server Settings' option under your problem account(s) > Click 'Advanced' button towards the bottom right > Select 'Global Inbox' option and check the 'Include this server when getting new mail' box.
This process should re-enable your account and allow you to get your missing emails.