StrokeIt brings out desktop while playing warcraft WIN7 x64

As the subject says, strokeit brings out desktop while playing warcraft (FILE: war3.exe).
This behaviour is really annoying, although I have checked and rechecked that war3.exe and Frozen Throne.exe is in the disabled apps list.

Right now everytime I want to play dota, I have to manually disable StrokeIt (right click on the systray icon).

Operating System : Win7 x64
StrokeIt version : 0.97

There are many applications that are started by an .exe file but their window is created by a .dll/whaterev. Beside that there might be occasions when identifying something by filename does not work reliably. Next time it dumps you to the desktop start a task manager (preferably Process Explorer) and take a look at the running processes. If there are other process started by war3.exe you should include that in disabled apps list.
Alternatively you could try identifying it by windows title using "Warcraft III" (without the quotes). That might work (or so I remember...).