I don’t see where you used the set focus or if you used it.
Did you do a Calibration? If you have a good calibration and use set focus in the top left part of what you are cutting you should get a better cut. If as is often the case with Proofgrade cutting the setting is the minimum to work, then any problem or inconsistency will not cut through. Many folk have discovered that when the sticker is in the lower right it is not always read well but upside down in the upper left reads better 
I discovered that even the perfect setting for a long cut is not so much when the cut is not straight. If you cut the speed perhaps by ten from the Proofgrade settings it could solve your problem.