The event case for the stop button shouldn't interfere in any way with the rest of the loops reading the true stop button value. I suppose you are reading the stop button value in your other loops using local variables for the stop button? If so, your stop button can't possibly have latching mechanical action. That means that it will stay true (depressed) until you manually click on it again or programmatically write its value back to true. Therefore, your loops should have no difficulty reading the true value for the control and terminating themselves.
You might look into some examples on Notifiers for a more robust way to send messages to various loops. Can you post some reduced example code that reproduces this issue? It won't help us to have your whole application, but if you can reproduce this with just two small loops or something, we might be able to recommend a direction to proceed in.
Jarrod S.
National Instruments