Bug#710028: further informations
The problem seems to occur when the terminal is losing focus, no need to switch desktop.
Bug#632846: gnome-terminal: window opens in background and doesn't get focus when --geometry= is specified
I just noticed that I have the same behaviour with gedit, epiphany and iceape. PS: Please move this bug to the appropriate place (or tell me how to proceed), I don't know how to do this (since it's my first bug report). Thanks.