"The machine Co ordinates of my X axis where it meets the 1220mm end of the sheet is reading 1230mm
And the y axis upper machine Co ordinates where it meets the top of the sheet at 2440mm reads 2514mm"
So it thinks X has moved 1230 mm but has actually moved 1220 mm, and Y has moved 2440 but reads 2514. Since it goes back to zero correctly it hasn't hit the end stops. Mach 3 works in steps per unit, so many steps per mm in your case. So if you asked X to move 1.23 mm it would actually move 1.22mm. Therefore you needs to increase the number of steps/mm it's set to by 1.23/1.22 = 1.0082. Similarly the Y number by 2.514/2.44 = 1.03033
To do this you need to open Mach3 and click on the "Config" menu, then select "Motor Tuning" from the list that drops down. You will get a window with a blue graph on a black background with various things you can change. At the top it will say X AXIS MOTOR MOVEMENT PROFILE, and at the bottom left is a white box with "Steps per" above it. Look at the number in it, with a calculator multiply it by 1.0082, then type the result back into the box and press return. When you do this the SAVE AXIS SETTINGS button text will go black - press the button which saves your change and greys out the text again.
Now click the Y AXIS button near the top right, and repeat with the Y axis factor. Save again. The Z axis probably needs correcting too, just repeat the same process clicking Z Axis. Then clock OK at bottom right to exit the menu. It's probably wise to close and restart Mach 3.
I think my arithmetic is right, but you may have to divide by those factors rather than multiply.
Also ideally you would accurately measure the actual movement of the cutter relative to the table over a shorter distance, say 50 or 100mm, to get the factors. This is covered in the manual in section 5.5.1, and there is also an automatic procedure described in 5.5.2.3 - though you still have to measure the distance moved.
Does your machine have leadscrews to move the axes, or toothed belt, or what? Axes with leadscrews are probably best set up by calculation as long as you know the screw pitch.