I'm using Matlab and Simulink for OS X. Whenever I edit a block in Simulink, my mac loses focus on Simulink (or X11) and gains focus on Matlab. In practice, this means that every time I edit a Simulink block and press "OK", Matlab pops up. It looks to me like the Simulink blocks are actually opened in Matlab. As Matlab isn't running on X11 anymore (THANK HEAVEN!) Matlab regains focus. This behavior is insert_strong_adjective annoying!
As of this, I would also throw in a request for a more unified Simulink layout and behavior on Windows and Mac. You should seriously skip the X11-dependency for Simulink. One of Simulink's strengths is being a highly visual application. It seems to me that X11 makes all that "visual behavior" ridiculously reduced compared to the Windows version. I'm sure you're all completely aware of this, I just hope that you actually do something with it.