I have some ortho4xp scenery that are symlinks pointing to a location on another drive, when I load in to x-plane, some of these are moved to the top of scenery_packs.ini by SAM. When I close X-plane, they are returned. I confirmed this having scenery_packs.ini open in notepad++ as it notifies when another program changes the open text file, and when I reload it I can see the changes. With the ortho on top all airport and overlay buildings are missing. I hope this can be fixed in a future release.
EDIT: I see now that the orthos are being added by x-plane as they were missing in the scenery_packs before, the problem remains that sam removes them after x-plane is closed so I can't move them down to where they should be for next launch, and sorry for posting this in the wrong forum, I see the bug reports forum now
Another edit: Still happening with 10 specific tiles for some reason, even when they exist in scenery_packs.ini before starting x-plane.