When you are jogging, can you use "step jog" mode, set the jog increment to, say, 1.0 inch, jog once and have the axis move that far? With "that far" being indicated both on the DROs (digital read out on the Mach4 screen) and by measuring the actual distance traveled?
What is the "Jog Rate" value (at the bottom of the "Jogging" tab)? If it is "50%" (I think that is the default), try setting it to 100% and jog again. Does it still work?
When you try running GCode, try a simple G0X1 type command (starting at position zero). What does the X-axis DRO show and how does the axis move? Then try "G1X1" (G1 instead of G0). Any difference?
If none of that works or gives you any hints, you can also post a "profile package" here (go to Help->Support->Package Current Profile).