I'm not sure when this problem started -- I switched my Mac to El Capitan not long ago, and I believe my Thunderbird was also fairly recently updated. Dealing with my email has often become a multi-step process, since after I send an email, I end up in desktop, and have to click on Thunderbird again. I have also not been able to keep multiple mail windows open for reference simultaneously -- screens appear to slide to the side and disappear, leaving me in desktop.