the behavior in standalone or launch from VS studio is different.
On the left of the screenshot attached you cas see the stand alone version. the '?' and 'x' on the top right corner have disappear, the background of the spy window is transparent.
On the right the one started from Visual Studio. It get my VS properties (black) and you can read in the spy correctly.
It's not blocker but it doesn't easy to use.
The shortcut used to launch standalone application : "C:\Program Files (x86)\Microsoft Visual Studio 11.0\Common7\IDE\CodedUITestBuilder.exe" /standalone