Are you pinning it down flat? Even Proofgrade material can swell a little bit over time due to exposure to humidity, and warp just a hair, and that will keep the cuts from being complete. The warping becomes worse on partially cut sheets, since removing the interior material takes away part of the stabilizing support and the forces of nature really tend to twist it.
If it’s cutting almost all the way through, I’d look for warping as the culprit. (And it might look flat, but if you can press down on it and it moves, it isn’t flat enough.)
I use these honeycomb pins to pin the material down wherever possible…it has made a world of difference in the cuts. 
Oh, and if you want support to take a look at it, you’ll probably want to print the Gift of Good Measure on Proofgrade material, flip it over, and take a photo or do a screen cap of the results so they can see it. Might save some time to have that ready.