Ok thanks to both now I know. I am attaching the flight plan after loaded from PFPX into P3D in the nav log. It looks fine to me not sure how PFPX can be responsible for anything if the Navigational Log is fine but you know better.After the flight plan is loaded into PF3 but before you connect, click the Adjust Altitudes button on the main PF3 screen and you will see where the XXX waypoints have been added.
Take a look: