At first it sounded like you had your X and Y axes swapped, which is easy to fix (in Ports and Pins/Motor outputs). But if you're talking about one single command in a whole string of them, then you might just be looking in the wrong place. Mach doesn't necessarily show you exactly the move that's happening right when it's executed - usually the numbers in the box are off by three or four commands. Does it seem to basically move in a circle, or is it doing something else? When you jog the X axis, does X move, or Y? If you zero the X axis and give it a MDI command like G0X20.0, does the X axis move 20 mm to the right, or does Y move?
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