I have a feeling that this has to do with your data acquisition being so slow.
If you are only doing one scan per minute, I suggest you do use the AI Sample Channels VI, rather than a continuous acquisition.
The reason is, in the VI you are using, LabVIEW ties up the processor when the AI Read VI is called, and it is waiting for the data to be available in the buffer. Since you are scanning at 1 scan per minute, it will have to wait a minute until the data is ready, and it will take control of all the CPU time in the process.
Depending on when in the cycle you pressed the stop button determines how long you'd have to wait until the AI Read comes back with the data, and allows the CPU to process the stop button.
Using the AI Sample Channels VI with
a 1 minute delay will accomplish the same task, but it won't tie up the CPU like it is currently.
Mark