Mark, I am going to forward this to the Shopbot team to get you straightened out.
I am not sure where you are located, but if it's cold maybe that's your problem. I am in New England, and my garage has limited heat. I had been leaving my Handibot in there, but the cold makes it bind up, and miss steps when you do a quick move. When the machine is super cold (below freezing) even really slow moves can cause lost steps. My first solution was to aim my space heater at it to warm it up. While that worked, it took a very long time to warm up. My solution now is jus to keep it inside where it's 70. When I use it, I just bring it in the garage. Once it's warm and on, it will maintain it's heat and not miss any steps.
What jog/cut speed are you using? I typically don't do anything faster than 2" per second.
For your limit switch issue, when are you seeing the issue? When you are homing the axes? I had an issue with one of my limit switches (or so I thought) and I realized that I had the Z up way too high when I ran the zeroing routine. The way I understand how the switches work is that some, or all of them are on the same input. So when I had my Z axis all the way up and I ran the zeroing routing, it started to move the machine in X and Y, thinking that it was hitting one of those limit switches. The machine would hit against the end of the X and Y and keep going, acting just like it wasn't reading the limit switches at all. The solution was just to lower my Z an inch or so and run again the zeroing routine again and everything worked fine.
Not sure if that's your problem, but it might be worth looking at.
I am not a Shopbot tech, just someone who's run into a few problems so take this for what it's worth!
I have forwarded this to the REAL Shopbot guys so you'll very likely get a response soon.