Is it buttons or switches? I used to forget to put a "PULES +" command on my switches. Once thrown, they continue to send key commands until switched off. You need a "PULSE+" command included to stop any repeats.
Start your profile and run the device analyzer to see if there are any switches stuck or flickering. If that's OK, run the event tester and see if anything is repeating. Run it anyway. As the Device analyzer will only report controller inputs and dx outputs. Not mapped key commands.
If you post your script. I would love to take a look. It's like puzzle.