Since I updated Thunderbird a few days ago, the SEARCH message function (Neither in the top bar that appears CONTROL +k) nor in the FILTER message field when one is placed in a folder, work. I know the messages are there, but SEARCH can't find them. It is one of the functions that I use the most and it is making it very difficult for me to work.
I have the same problem and found a fix. Rightclick on your inbox, choose "open in new window", and then close the old window and search in the new windows should be working.