Why does my Y-axis calibration not change the actual output size?

I'm using an Omtech Polar laser with a Ruida controller and LightBurn. I need precise dimensional accuracy, but my Y-axis travel is consistently about 2% short—a 50×50 mm square measures only 48.9 mm vertically. I've used the Calibrate Axis function in Machine Settings to generate a new Step Length value, and I've confirmed it's saved to the board. I even tried manually lowering it from 43.xxx to 20. However, regardless of what value I set, the vertical measurement remains 48.9 mm. Is there something I'm overlooking?