Hi Tim,
Without seeing your VI, it's hard for me to offer a solution, but I think I have a basic idea of your problem. Because of data flow programming, the method of execution in LabVIEW, a while loop will not execute until all inputs to that while loop are available. Similarly, data will not be released from the while loop until that loop has finished execution. What this means is that you cannot pass data between loops with wires. To pass data between loops while they are executing, you can use local variables. These allow you to read the value of a control or indicator from multiple places on your block diagram at the same time. I am attaching a very simple example in which one stop button stops the execution of two parallel loops by way of a local variable.
I hope this helps!
Sean C.
Applications Engineer
National Instruments