First that whole case structure needs to go bye bye or feel free to post it over on breakpoint in the Rube Goldberg thread. It outputs True in the True case and False in the False case. Just set the Mechanical Action on "STOP" back to Latch when released and wire the AND output to the conditional terminal. Delete the other "Stop" Local too,
Next place the "Stopped indicator outside the event handleing loop so that it is written to true only after the loop completes- that really improves only the readability of the code but does make it obvious that the ACQ loop completion is dependant on the event loop. When you put all the rest of the code back you'll thank me for that.
then get a case in the Event Structure to handle the application close? Filter event and discard the app close event. Someone hitting the Windows Red X will leave you in a bad state unless you do that (See also final point)
Now your FP values will always be as expected UNLESS someone hits the abort button- then all bets are off and the system can start in an unexpected state causing unexpected results. SO DON'T DO THAT anymore. Rip off the abort button- It is a debug toy only and can really cause trouble and hair-loss, as you are finding out.
Final Point: Are you really sure you want to disable a stop button? (I think I've shown that ignoring Stop's output and depending on your other condition as determined in a stop value change event is preferable but I am making a point here) Users expect applications to behave in "Normal" ways. "Stop means Stop!" and "Stop is always a valid thing to do". You are almost always better off performing a graceful exit that releases all resources and cleans up after itself.
So a proper QSM design pattern implementation will improve performance and make maintanence a whloe lot easier when the Stop event enqueues (opposite end) a Exit command where Exit places everything in a nice clean state.
@Cameron- I'm sure you would have followed the "Use a latching Stop" idea to its eventual simpler "and output the AND result" had the RG Case structure not obfuscated the code nearly beyond reading. Allways be wary of boolean case structures- many sins are hidden in them. If a select can substitute for the case, use select and there is no hidden code.