nyborn,
I took a look at your code and neither stop button is successfully connected to either stop terminal.
1) In your while loop witht the sequence structure inside, the wire doesn't connect the stop button and stop terminal.
2) In both while loops the stop buttons are indicators. They need to be controls. To change them right click on the buttons and select "change to control".
For future reference, it helps to comment the code and clean it up (organize block diagram and front panel) as much as possible before posting it to the forums. The cleaner the code and more commented it is, the easier it will be for the community to understand your end goal and help you solve your problems. Good code with explicit questions also increases the chances of a response to your forum post. Let us know if my suggestion solved the problem.
Best Regards,
Chris C
Applications Engineering
National Instruments