With the latest thunderbird, the string to search for in the config editor to set it to check all folders for new email has changed from:
mail.check_all_imap_folders_for_new to mail.server.default.check_all_folders_for_new
As detailed here: http://kb.mozillazine.org/How_do_I_check_for_new_messages_in_other_folders Which caught me out for a while as I was looking for the old one in the config editor.
Sick of having to click on a window, then click on the button you think you already clicked on? Paste this into a terminal:
defaults write org.x.X11 wm_click_through -bool true