Here’s a tip that I learned through bitter experience.
When entering a flight plan into the default G1000 (or even the G530), do NOT pause the simulation while manually entering the way-points or procedures. While it appears to work fine if you enter the fields while paused, occasionally (but not always) the GPS gets confused and corrupts the visual display – sending tracks between way-points to Timbuktu and back! It is not only the graphical map display. The flight plan itself gets corrupted even if the listing looks OK in the MFD.
I don’t think this is a bug since it is logical to assume that a bit of processing goes on in the background when calculating the GPS display. If X-Plane is paused, presumably whatever processing it is doing does not happen. I am not sure whether this has always been a problem or only in recent versions. Certainly the problem is in X-Plane 12.11.
So learn from someone who spent an entire day tearing his hair out in frustration – DO NOT PAUSE X-PLANE WHILE ENTERING A FLIGHT PLAN! 😤
Provided X-Plane is un-paused, entering the exact same flight-plan works perfectly.
If time runs away with you because it took so long to enter the flight-plan, reset back to an earlier time once the flight plan has been entered and saved.