In the Logi profiler enter the keystroke as a "new keystroke" rather than a "command". When entered as a command the profiler just plays the recorded keypress over and over again when you hold down the trigger for instance.
Also avoid using "commands" for modified keypresses i.e. CTRL_E, sometimes the modifier key release isn't registered.
Logiprofiler isn't to bad if you try and keep as many of your assignments as keystrokes rather then commands, it's just a shame you can't give the keystrokes a name to remind you of what they do