When you have created a flight plan outside the sim, with any external tool/flight planner and you load this flight plan into MSFS, you will see, it works normally. But when you, change anything after (parking position, terminal procedure, runway, …), the flight plan will be automatically re-created and doesn´t normally look like the original one, which you have imported.
This is a MSFS limitation and has nothing to do with the navdata or the tool, where you have created the flight plan. It´s a automatic process, and you have no chance to avoid this.
Cheers,
Richard