It's difficult to reply, if you don't supply a specific case of which scenery and which gate you were located.
In any case, it's not really a GSX problem: it's not the GSX vehicles are "sunken", it's more like the *scenery* that is "raised", to overcome z-fighting on ground and, because of the round earth issue, you might have parts were the raising is more visible, and this happens in our sceneries too.