If that works, and similar commands on all the axes check out, then it's probably not a mechanical problem with your machine. That leaves your Mach3 settings and BobCAD to scrutinize. If you run a short piece of code like you suggest, what happens? Zero your machine so it has room to move a few inches in X and Y, then try something with motion in two or more axes, like:
G01X3.0Y2.0F20
X0Y0
X3.0Y2.0
X0Y0
X3.0Y2.0
X0Y0
X3.0Y2.0
X0Y0
X3.0Y2.0
X0Y0
X3.0Y2.0
X0Y0
X3.0Y2.0
X0Y0
X3.0Y2.0
X0Y0
(etc.)
See if it comes back to zero after 10 minutes or so of that. If so, (and if the first test was successful) then it's probably not a problem with Mach3.
That leaves BobCAD - if that's your problem, post a question in the BobCAD forum, and be as specific as you can about what goes wrong.
Andrew Werby
ComputerSculpture.com — Home Page for Discount Hardware & Software