How to Calibration

Does your machine otherwise burn dimensionally correct shapes? If not, then I’ll assume this is a generalized problem.

Design a rectangle as large as can be accommodated in your laser. Use framing to make sure it fits within the bounds since your calibration seems sufficiently off that you’re in danger of overrunning the boundaries.
Burn the rectangle
Measure width and length of burn
With the laser connected to go Edit->Machine Settings->Calibrate Axis and enter values for nominal size (as designed) vs actual measured size. Repeat for both axes
Once complete, run a test for another rectangle. Bigger is better. Measure. If the dimensions are still off then repeat the calibration with the values of this test.

Rinse and repeat until you have acceptable results.

If your machine otherwise burns to dimension, then it may be a design issue.