Dave, upon a little more testing today. I can get the debounce down to less than 250 and be relatively consistent with the various operations. I am understanding most of it better. I do have a question about noise. Presently I am not running any caps on the inputs from my probe. i have read that using a .01 -.1uf cap can help with the noise issue. Is this the same as using the debounce or does it quell the noise some other way? Would this be an advisable way to help the situation in your opinion? If so, which value cap would you use of those 2 mentioned?

Well I went ahead and placed a .1uf cap between the probe pin and ground on the controller and reduced the debounce to 0 (was working ok at 50). So far so good. I still get a stop occasionally but it is operating much better. But I dont know if it was the cap or just a better understanding. I think the cap must be doing something as it was very hard to complete a sequence with the debounce on 0 before. I can repeat measurements after retracting the probe and placing it back and remeasuring it. The measurements come out the same. If they do vary it isnt til the 3rd digit and mostly only the 4th, way accurate for anything I am doing.

Welcome to the wonderful world of herding electrons - I'll skip the EE discussion and keep things empirical.

The cap is acting in conjunction with a resister in the BoB to create a simple filter circuit.
The higher the cap value, the larger the amount of filtering added.

Adding the cap is an electronic way of doing what the mach software de-bounce setting is doing.
So the effects from adding the cap and the debouce setting will be additive  - and this matches what you are seeing - with the cap you need less software filtering.

If you are curious to learn more, you can google "RC time constant".
Here is reasonable tutorial I spotted from the google results:
http://www.electronics-tutorials.ws/rc/rc_1.html

Dave