In this, the lights are mounted normal and not hover over the runway.
Therefore, your statement is not true that this is normal!
My statement is obviously true because, as I've said, they are raised A BIT, to prevent flickering.
You haven't said how much they were raised in YOUR installation so, I couldn't say if you were seeing was the normal, very small, rising over ground that the light ARE supposed to have, or something much larger, which would indicate some kind of a problem.
I ask you to give me a solution or I want my money back and I uninstall also like the addons in this case again.
Since all our products are available in Trial, you cannot obviously ask for a refund.
And even more, considering YOU said yourself the same scenery works correctly on another system, under P3D too. This clearly indicates the scenery doesn't have the slightest problem (which should be quite obvious, since it has been released many years ago, and nobody else reported this problem), that it works in P3D, and your problem is caused by a specific of your installation, not by the scenery, that's why you can't ask for a refund.
You might try resetting all your settings, by removing the following folders:
%PROGRAMDATA%\Lockheed Martin\Prepar3D v2
%LOCALAPPDATA%\Lockheed Martin\Prepar3D v2
%APPDATA%\Lockheed Martin\Prepar3D v2
%USERPROFILE%\Documents\Prepar3D v2 Files
In fact, this is what LM suggest to ALWAYS do after installing a new P3D version, and if you don't do that, you'll see all kind of graphic anomalies.