I'm having the same problem with gtk3 terminal emulators (roxterm-gtk3 (2.6.5-1), sakura (3.0.4-2)). And gtk2 terminal emulators (roxterm-gtk2 (2.6.5-1), lxterminal (0.1.11-4)) are working fine.
This guy also had problems with gnome-terminal and gedit. http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=656032 Here's how this problem occurs on my machine: I'm using wmii window manager. I launch sakura, for example, switch to an empty tag, and switch back. The sakura window get back focus, I can still type, but the cursor never blinks. And other applications still think it not on focus, I can't use ibus with it now. To get focus really back, I can switch to an non-empty tag, then switch back, the cursor starts blinking again, and ibus gets working. libgtk-3-0 version: 3.4.2-2 Please fix this. -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". Trouble? Contact [email protected]

