I've been having problems with Prepar3d V2. Some I've solved, some I have to work around.
SimLauncher is a FREE workaround that I like.
SimLauncher - it works with both FSX & Prepar3d to setup your flight & launch the sim.
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The newest file is supposedly on FlightSim Eindhoven, but that download link was bad when I tried it.
Go to Fly Away Simulation to get the older version. It should automatically check for the latest update. Download that, and your in business.
AN ABSOLUTE MUST!!!! - You must download & install a free program called MakeRunways 4.674. IT IS LISTED UNDER the FS2004 section.
You need this for BOTH FSX and/or Prepar3d V1.x or V2. Put it in the FSX and/or Prepar3d root folder before you run it. It'll generate 2 files.
I don't think that it was really made for Prepar3d V2, but with only the smallest amount of effort it will work. If I recall correctly, I had to make a empty text file or two with the names of files that it was looking for. It then overwrote the non-information in them. I also think that there were problems getting the paths right, but that might have been due to my installing Prepar3d V2 in a different location.