I'm not sure whether posting to this existing thread is right or not, but it seems that the OP was experiencing the exact same problem I am now.
I've had numerous issues getting this scenery to work as well as it should, mostly down to a broken FTX Global install, I think, but I've this last elevation issue remaining
To really rub salt into the wound, my first install of Skiathos didn't exhibit this issue, but a few uninstalls and re-installs later... Sigh.
I've searched high and low for offending BGLs - There's one FTX_VECTOR_APT\scenery\ABP_LGSK.bgl
which I've added disabled via the configuration tool troubleshooter. The only other thing I can find by searching my entire disk for "LGSK" is MyTraffic\Scenery\BR2_LGSK.BGL
which I have also disabled by adding .OFF to that filename. But still the issue persists.
I checked the Scenery\World\scenery folder, and the JSI_AFX_ALT file is present, and if I try the file supplied about the overwrite indicates that the two files are identical.
I've run the FTX Vector tool multiple times in desperation, but no joy there either! I am at a loss as to why this is behaving the way it is... This is the ONLY Skiathos scenery I have, or have ever had, as far as I can tell the only BGLs in the equation are the default P3D base scenery, and this 29Palms one. All I can think is that there's something cached somewhere with the wrong data?
Any advice that you can offer would be greatly appreciated! It looks like a lovely bit of scenery, but man it's fought me every step of the way so far!