Ok, well the first thing I would do is the following 2 tests.
1) Go to the S3D Machine Control Panel, click on the Jog Controls tab, and then hit "Home All". Note where the printer moves to. Next, go to the Communication tab and enter "G1 X0 Y0 F3000". Where does the printer move now? Does it stay in the same place or does it move some to a different place on the bed?
2) After you have done the steps above, then go to the Jog Controls tab and use the X and Y jog buttons to jog the toolhead to the maximum XY dimensions of the bed. Keep track of how far you move the print head. You can also use the position readouts in the top right of the MCP if you want. Once the nozzle gets to the far corner of the bed, record how far it moved in the X and Y axes. You could also measure this with a ruler or something, but I find that actually jogging it in the software is more reliable, since you get a better feeling for the clearances of the nozzle as it moves.
If you do those 2 things, it should be easy to figure out what settings to change
