You did apply the flattens mentioned in the readme, correct? If so, I don't know what is going on for you - if not, well, then I guess you have some work to do!
I couldnt figure this out. My FS9 is on an exterior drive, and the scenery.cfg file didnt show my new KPLN files. But I found in the FS9 folder another scenery cfg file and found the KPLN sections and was able to install the flattening section and the +1 layer. Looks brilliant now. I figured it was something I had added to FS causing the cars to submerge a bit.
Bill