Having a stop button is senseless the way you've written the VI. It will automatically stop when you get to the last frame of your sequence structure and the stop button will be ignored until then because a sequence structure ALWAYS executes every frame. If you want the ability to stop early, you need to remove the sequence structure and use a different architecture. A state machine would be ideal. Look at the shipping examples and the different design patterns (File>New...).
Most likely, the stop button will get read while the sequence is still executing, giving a high chance that the conditional terminal receives a FALSE after the first iteration (race condition). THe stop terminal belongs in the last frame in a sequence like that.
Avoiding the seiquence and use a state machine will be much better as Dennis already mentioned.
Of course you use the stop primitive, which aborts the VI before the conditional terminal even gets a chance to act.
You should really never use a STOP primitive except in emergencies. Once the VI has competed all its code, it will stop naturally.
Your tight inner loop needs a wait statement (see also this link).
The small sequence frame on the left has no purpose. It does not enforce any specific execution order and none is needed anyway.