I had the same problem and fortunately I found the solution. You have to run StrokeIt 'as an administrator' for it to work with some applications like Notepad++. 'Shutdown Strokeit', and then restart it as an administrator and it should work.
You don't have to run StrokeIt as an administrator, you just have to run Notepad++ manually. The problem occurs, when a program is started from an updater or setup routine with elevated privileges.