Curious! Something in your airport (or that is affecting your airport) is conflicting at Layer 40. This has not been reported before, but I'll keep it in mind should anyone report similar difficulties. (I see nothing in the ADE file that should cause this.)
Placing the lines in different layers should not have any effect. With ground polys, layering is used so as to be able to control which texture gets placed on top of another. The GPs all get placed at the same elevation and can be superimposed in a single layer.
Re the CVX file, first of all, I note that the flatten elevation is 56.997m while the airport elevation is 57m. While this difference won't materially affect the appearance of the rendered airport, it may be enough to cause GPs to disappear at certain angles.
Also, since the flatten IS in the ADE file (hidden, which is why I didn't see it yesterday), I spent a little time exploring why it didn't compile for me. What I discovered is that, if I compile the airport for P3Dv2, the flatten is generated. But, if I compile for FSX, I get an error message "The system cannot fine the file specified" and the CVX file is not generated. I ignored this message yesterday, assuming it pertained to some model placed in the file. Apparently, it relates to CVX file generation. Over to you, Jon.
Don