I can't guess why this would be intentional, since docking with stations doesn't clear nav points.

How can you be sure that docking with a station doesn't clear your nav points, since you can't see the nav point while in the station?

When you launch from a cap ship, do you get a different nav point?

I bet it only happens when you have a mission.

Then, if you launch from a station or cappie, you route is re-set to mission destination...