The marshaller will ALWAYS put in the correct place.
The "correct" place, lacking more precise information from the scenery (this kind of information is only available with FSDT scenery), is with the airplane center in the center of the parking, which is exactly the SAME spot as if you were using the default "Go To Airport" menu.
So, your question doesn't have anything to do with the GSX marshaller or the positions it directs to, but rather why a certain jetway on a certain scenery you use doesn't work when your airplane is parked in the default position ( which is the same, regardless if you went there the the "Go To Airport" or GSX marshaller ), so it's not relevant to GSX in any way.
Now, if the scenery is an FSDT one, it would be best if you said which one it is, and which gate you are referring to, so we might check it.
If the scenery is non-FSDT, you'll find out that, if the jetway didn't move in the spot GSX directed you to, it would have been the same if you went there with the "Go To Airport" menu.
With FSDT sceneries, we can CHANGE, parking by parking, the position where the marshaller expects you to be, but with default or 3rd party airports this is not currently possible. More precisely, we would have to provide a customization "corrective" file for each 3rd party or default airport, to improve on the same situation you would have encountered by default, if you never had GSX to begin with, but this is not feasible unless we started to charge by airport, which is not we intend to do.
Instead, future GSX versions might allow you to customize this.