My Registries are fine....
If the installer doesn't install into FSX, it means they aren't. Note there are TWO different registry entries for FSX, you might believe they are fine because you might have checked only one of them, start REGEDIT and check the following keys:
HKEY_LOCAL_MACHINE\Software\Microsoft\Microsoft Games\Flight Simulator\10.0
HKEY_CURRENT_USER\Software\Microsoft\Microsoft Games\Flight Simulator\10.0
And be sure they BOTH points to the folder where FSX is really installed and if they aren't, fix them with the correct path.
If you did everything right, since you *have* Prepar3D, the installer WILL show "Prepar3D found" anyway but, it's a request to install it there or not. If you say NO (which is the default), they will install into FSX.