I've seen this in several airports recently, but let me start with LatinVFR - KSNA John Wayne because it's the most recent for me.
Essentially, when I load any aircraft from the P3D scenerio screen into a gate at KSNA P3D locates me correctly (i.e. jetways are in the right place, my nose wheel is on the parking center line etc.)
However, when I open GSX it doesn't recogbize that I'm in a valid parking spot and wants me to pick a spot and either taxi to, or warp to it.
When I select the spot I had P3D place me in, then select "Just warp me there" my aircraft gets moved to a place that is somewhere in between parking spots, and sometimes (depending on the spot I choose) into the terminal building.
I've done tried removing the two folders:
C:\ProgramData\Lockheed Martin\Prepar3D v2\SceneryIndexes
C:\ProgramData\Virtuali\Couatl
The reindexing most certainly recreates them, but the problem persists.
For curiosity sake, I also used the "Simple Airport Scanner" from scruffyduck to see if there were any other KSNA afcads in play in my P3D v2.5 installation. There are not, there is supposedly only the one from LatinVFR.
As I said, I know this has happened with other addon airports, but not all.
Any thoughts on the possible issues that remain?
I hope I provided enough information. Thanks in advance!