I had this happen on the Community Fly-In, the GNS530 (modded version) shows both artificial waypoints, what is weird is that it shows the last leg as active prior departure.
You can give it a try by downloading the flight plan from the fly-in, load it in the world map and without changing anything just press Fly.
I then loaded it up in LittleNavMap, changed type to IFR, exported as PLN again and loaded it in the world map, all was fine with the flight plan from then on.