I have the exact problem with an Ubuntu 14.04 server and OSX 10.11 client. I set single application mode to launch /usr/bin/xterm. Moving the window incurs a 3 or 4 second delay before the application is responsive again. For the app I want to use (MATLAB), this makes single app mode completely useless for me as well. It pops up lots of small windows as GUI elements and these also have a slightly faster 1 or 2 second delay.