John, if you are getting an error message when loading all flight plans, exit PF3, go to your PF3 folder, right-click the PF3_Register.exe file and select Run as Administrator. Wait a few moments and start PF3 and try again.
If some flight plans will load and some won't, go to the folder where your flight plans (.pln files) are saved and find one that won't load, zip the pln file and attach it. Maybe as Dave said there is a problem with the format.