Darin,
I noticed the following quote in your post "When I drew these and made the toolpaths I adjusted for tool width". What? Drew the toolpaths with what software?
If you enter MX 0, followed by MX 2, does the X axis move exactly 2 inches? That is the key question. If that works, the shopbot is operating the X axis correctly. Check the other two the same way.
Now if its not cutting what you expect, the phrase you entered "When I drew these and made the toolpaths I adjusted for tool width" bothers me. If you are doing your design in Vectric products (VCarve Pro, or Aspire) you should NOT compensate for the size of the bit. The design software does that for you. So my question is what software did you "draw" the toolpaths in?
I do most of my designs in the Vectric software (great stuff, I can highly recommend. Worth the price!). In that software you draw what the result should be: a hole of a given diameter, or an island with the material removed from the perimeter. Draw these at the size you wish the result to be. Then when you run the toolpathing operations of the software and select a bit to use at that point, the geometry of the bit will be taken into account. Then you can use any bit and get almost identical results.
There I used the word "almost". And that is where experience with the machine and materials comes in. As a beginner you should be getting accuracy of about 0.02 inches. Later when you figure out what you are cutting and how to cut it efficiently, you will learn other techniques to improve that accuracy. I have been stunned at the accuracy I can get out of the BT-32 Alpha. Mine is an older machine with a lot of years of use. Its still amazing
Hope that helps-
D
"The best thing about building something new is either you succeed or learn something. Its a win-win situation."
--Greg Westbrook