There's no FSDT San Francisco airport, maybe you wanted to say Flightbeam.
Whenever you see a misalignment from GSX and the gates, it's always a conflict caused by another scenery. The most common cause of conflicts are AFCADs that comes with AI Traffic product.
You can use the GSX parking editor to see the name of the AFCAD in use, which should be the one that comes with the scenery.