Before we go too far with assumptions... could you post a link to a pic of the situation? Most times, as with all cam systems it's driver error. Reason being, on a clean install, most ops will error to leaving stock. That said, many will argue for the so called "high price" of the package , it should know exactly what to do - for you. I would argue that for the "high price" I want options of what to do. It may be leaving the spot due to the limits of the material removal settings (stepover, doc, toolpath choice, etc...).
Depending on the operation type you have many choices. Operation type, and pic should do the trick here.
-- Bill