Thanks for the troubleshooting, I will give the FS9 flightplans a go and see how that works out. By the way, I was able to load a flightlan created using a different flightplanner and that worked. The only error I got was that PF3 complained that my first waypoint was too close to the departure airport. Upon getting to the edit page though, I got a bunch of numbers and all zzzz in the edit boxes to the right. I was too sleepy to continue so I just shelved it for the night. I will try again with the FS9 flightplans and report back. Great work guys!
Try running your fpls through FSX and getting FSX to re-generate them as it were. Then that should be ok for a work around for the moment. zzzzs certainly don't sound right though so try fs9. FS9 still rules btw! Almost all developers still prefer to use FS9 xml code even for P3D!! Regarding being nagged for having waypoints too close you can turn that off, Options #1 under misc options. It rarely affects the fpl.