Hi, I get this problem too. Happened with Cubase 7 right after upgrading to Mavericks and continued even after deselecting the "Displays have separate spaces" option in System Preferences. Was upgrading to Cubase 7.5 anyway and it seemed to avoid this problem until my first reboot after installing 7.5 when it appeared again.
Upon activating any other device (Mix Console, VST Instrument Rack) the Project window deactivated but the new device window doesn't appear. I can only get it to appear by activating the Windows dialogue box (in the Windows drop down menu).. Anyone else still getting this problem?