I suspect part of your issue is the use of a Bush Trip that may or may not have been modified by a fourth party - based on your earlier post.
Here is my configuration, same as yours. Navigraph Hub (updated from NavData Center per Navigraph notices sent to subscribers), same AIRAC release.
Japan Tour.pln which I saved originally from when it was an Active Event long ago. Loaded into Little Nav Map, but has four missing waypoints.
Nonetheless, look at my World Map - clean. Even the same plane as yours.
I’m concerned that someone actually repackaged an Asobo authored flight plan and resold it, but that’s a different issue to follow elsewhere.
Try this copy of the Japan Tour. Maybe it will help.
LiveEvent.PLN (7.8 KB)