That can frequently happen if there is slight warp in the material, or sometimes if you live in a high humidity area…it causes draftboard to swell slightly.
To make sure that the material is flat on the bed, I like to use these Honeycomb Pins to pin down the material. That takes care of any warp very well.
For humidity related swelling, it’s possible to create your own Custom Settings where you slow the speed down by about 5-10 points. It will generally enable complete cut through in one pass instead of taking two to complete the cut. Instructions for how to save your own Custom Draftboard (or any other material) settings are here:
Working with Manual Mode
Once you set them up you can click on them and they load all the settings just like the defaults…one click.