You could do this in eoither of two ways. The most straight-forward is the case where you have a state-machine of some sort handling the button presses. All you would have to do is insert a local variable of the Pause/Run button in the case structure that is executed when the Start/Stop button is set to the "Stop" position. The local variable would allow you to force the switch into whatever state you want.
The other possibility is that you might want to do it in a subvi. In that situation you'd need to pass to the subvi a reference to the Pause/Run button and use the "Value" property to turn it off. The disadvantage of this approach is that according to NI using property nodes to set the value of a control is much slower than writing to it directly with a lo
cal variable.
If you have specific questions feel free to follow-up. Also if you could post the pertinent bits of the code in 6.0 format I could give you very specific recommendations.
Mike...