If you are seeing a difference between the two it is entirely possible that your changes are not being applied to the cutter. You'll want to figure out what's going on there. My software (different than yours) has a check box to either allow or not allow the program to control the cutter settings. I personally do the cutter setting directly on the cutter. Some budget cutters do not have the ability to adjust any of the setting manually on the cutter. I never trusted the software to be completely trustworthy and it seemed prudent to make sure my cutter was doing what I told it without the possibility of some weird thing happening. I'm less trusting than some so your mileage may vary.