GSX works only with AFCADs that are self-contained, so they include everything that GSX needs to work on it. It won't go through multiple active AFCADs, but will only use one at any time.
If the AFCAD you use only has corrections, GSX will use only the "complete" file related to that airport, which is usually the default one.
A possible solution might be loading the stock data into the add-on AFCAD using ADE, and save it back, creating a self-contained AFCAD.