I obsverved this same issue when I (mis-)used a flightplan from a Bush Trip just for normal free flying. In my case, it’s the original Japan flightplan included in a Payware package by RosiG2. It’s shown properly when I load it into Littlenavmap, but with the lines going North as above on the MSFS flight planner. When I continue to the flight, the GTN750 shows a straight line from the initial airport to the final one, exluding the intermediate airports.
Now, that LittlenavmapVR works great in VR I can use Littlenavmap in the cockpit for navigation but would still like to see the proper plan on the Avionics.