I am using ubuntu 14.04, with metacity, but the same bug was happening also using Cinnamon.
Basically I have a bash terminal in full screen mode.
If I use an other program, and this program opens a modal window, this modal window does not get the focus, but looses priority and the full screen terminal window appears in the front, making me use alt-tab to get again focus on modal window and the program I was using.
This happens only if there is a full screen window active in the back.
How to avoid it?