When I uninstalled GSX and reboot my PC my 3rd party jetways return with no problems. so, I don't know what GSX might be doing to prevent the jetways from showing up for the 3rd party jetways.
It would be best if you clarified what do you mean with "3rd party jetways".
- If you mean custom jetways using the default CTRL+J method, it's NOT possible GSX would make these to disappear, unless YOU do an exclude file for each airport with the editor. None of these jetways are affected or replaced automatically.
- If you mean SODE jetways in 3rd party sceneries, surely GSX doesn't change their files and, normally, is not even possible to replace them if you don't remove their SODE XML files manually.
So, in both cases, unless you did lots of things by yourself, is not possible that GSX could affect 3rd party jetways.