The StrokeIt will work better if it work with HotKeyboard freeware. You can download a free HotKeyboard from http://www.hot-keyboard.com/. With HotKeyboard you can assign any hot key to perform many actions for example to open folder, open file or any program. After you open any program by hotkeyboad,If you press hot key again, the existing program will be switch (active) instead of opening the new windows.It can solve the problems for StrokeIt, because if you assign any mouse gesture to open the program directly from StrokeIt. The StrokIt will open the new windows of the program instead of swiching to the existing one.
Conclusion :
1.Assign any hot key to open the file, program or folder by hot keyboard.
2.Assign the this hot key for the key stroke in the StrokIt. (you should temperly disable the hot keyboard firt.)
3.Assign any mouse gesture as you want.