For a while I couldn't drag emails to other folders in Thunderbird, which was very frustrating and made organizing my email very slow. I had to right-click on the message and use the 'Move to' option. Which is especially annoying if you organize your email in a nested folder structure.
It turns out the problem was AllTray, an Ubuntu application that lets you minimize any application to the system tray. So until I find a compatible solution, good-bye to Thunderbird in the system tray.