Hey suspencefull,
You are probably going to have to think about re-designing your code. Your pulse train is not continually generating because you do not have it in a loop. When you use the DAQ Assistant to create a continuous pulse train, LabVIEW will prompt you if you want it to automatically add the loop. You must have deleted it or chosen not to add the loop.
There will, however, be problems though when you add the loop back in. The SkipColor sub VI will not finishing executing until the loop is finished and therefore you will never move out of the first frame of your sequence. I would suggest redesigning your code so that these thing can occur in parallel.
Please let me know if you have further questions.
Regards,
Chris Delvizis
National Instruments