Sounds like some of the problems you might be having are due to warping in the wood - it doesn’t take much to keep a spot from cutting completely through.
If you have strong magnets they can help, but I have better luck using these Honeycomb Bed Hold Down Pins, since I live in a very humid area, and these tend to hold the material down better when it’s warped.
The other thing that you can do is slow down the cutting speed in the Manual settings by about 5-10 points. That should finish the cut completely, even if you have up to a mm of warp in certain sections of the board.
It’s a bit tedious to reset them manually, but not difficult - they give us little sliders to use in the Manual settings. When you have a Proofgrade material specified and switch to Manual, the Proofgrade settings are already loaded into the slots, all you have to do is tweak them.