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I'm a bit confused about the "STOP" buttons, I only saw "Abort" buttons in the 22errors.vi which is what I am assuming is the top-level VI. I downloaded and ran your program in LabVIEW 6i (I had to cut out all of the Data Acquisition VIs because I have a newer driver version) and I was able to stop the VI using the "Abort" button without problem. What buttons in particular are not working and are they functioning at all? Do they simply do nothing when you press them?
I would suggested that you cut the VI down as much as possible, leaving only the queue that changes the state, and watch the VI run with highlight execution. This will likely help you pinpoint exactly what is going wrong.
The problem seems to be that one of your main loops is stuck in a subvi with a loop, Measure Frequency.vi or Read Scale.vi. These VI's dont know that you have pressed the stop or abort buttons and so they will try to complete there tasks. Until they return the main loop will never get around to performing the Stop or Abort task.