Are you on Steam or Microsoft Store version?
Steam
Do you have any add-ons in your Community folder? If yes, please remove and retest before posting.
No. Tested with and without.
Are you using Developer Mode or made changes in it?
No.
Brief description of the issue:
MSFS “World” Screen not handling flight plans generated externally. Adds all kinds of crazy waypoints. Does not use correct (High / Low) routes, and if you select the correct one, MSFS re-generates the route.
Provide Screenshot(s)/video(s) of the issue encountered:
Will do so in post.
Detail steps to reproduce the issue encountered:
Will do so in post.
PC specs for those who want to assist (if not entered in your profile)
Intel Core i7 950, 24 GB RAM, GeForce RTX 2070, Windows Pro (64 Bit), 250GB SSD, 2TB HDD
Build Version # when you first started experiencing this issue:
Current build as of October 4th, 2021.
Did you submit this to Zendesk? If so, what is your ticket #?
Not yet.
I use Navigraph (desktop version) for my flightplanning.
I was having problems with a saved flight plan from PHNL - PHTO here in Hawaii. The flight (IFR, 15000’, C208B EX) would go along just fine until I started approaching PHTO. When I got near, it would overfly the PARIS point, then fly on to KENNZ, at which point the aircraft on autopilot makes a 180, goes back to PARIS, then back to KENNZ, and continues on.
Today I decided to redo the flight plan. Same PHNL - PHTO. Low Enroute Airways. The type route is this:
PHNL/08L MKK4 MKK V15 BARBY LYCHI1 PHTO/KENNZ.I26
I dialed in Runway 8L. MKK4 departure. then on the arrival end, LYCHI1 arrival, and ILS RWY 26 (KENNZ). Went to export the file to a .pln - selected my cruising altitude as 15,000’. Saved the PHNLPHTO.pln file to my special “Flights” directory.
Went into MSFS, it loaded up to the Hangar. Clicked on the World, hit spacebar twice to bring up the “load flight plan” dialogue, navigated to my folder, and selected my PHNLPHTO.pln. I’ve attached a screenshot of what it looked like when the flight plan loaded up.
The first thing I noticed (this happens a lot ) is that the “High Altitude Airways” is selected, even though I specified “Low Altitude Airways” in my plan. The second thing I realized is that I must have dropped acid or something while creating my flight plan. Either that or I secretly got drafted into the Coast Guard, and we’re looking for a boat or something. 
Here is the flightplan that was generated by Navigraph:
PHNLPHTO.pln (13.4 KB)
If I change it to “Low Altitude Airways” and put in my desired starting point - Gate(Parking 347 – GA MEDIUM) in the MSFS Flight Plan screen, then I get this:
Better, but not what I was looking for. if you’ll notice - there’s two waypoint “PULPS.” If I delete one, the MSFS Flight Plan shows only one “PULPS,” which I never put in there in the first place. If I try to delete the other one, it regenerates the 2nd “PULPS.” (shrug) MSFS problem perhaps?
I double-checked my departure in Navigraph just now. I selected MKK4.MKK. I overlaid the departure onto my flight plan. You can see “PULPS” there, and see that it is NOT selected.
I loaded my flight plan into Volanta, and this is what it looked like:
If I copy the type route from the beginning of the post an paste it into Volanta, the route looks like I would expect it to:
(I was able to fly, but I had to delete practically everything in the FPL screen of the G1000NXi.
Am I doing something wrong? If I am, please let me know. I hold a FAA Dispatch license, so you’d think I could put together a flight plan.
Thank you to all who made it to the end of my manifesto.