John,
Sound to me like the vinyl is starting to move before the knife is all the way down. This could be caused by a sticking knife holder due to dirt or age. In the owners manual there is a section on "overcut". You can adjust the overcut from 0 to 10, 0 being off and 10 is maximum. Each unit equals about 0.1mm or 0.004". Although you only need this for the first cut, adjusting the overcut will effect all cuts. This might help compensate if the part that's missing being cut is 1mm / .040" or smaller.
This photo is right out of the manual. I hope this helps.