It's likely the AFCAD which is now active is not the same which was active when you customized the jetways, but for some reason GSX is not reading it, but the sim is.
The most common case of GSX not reading the active AFCAD, is if you (or a 3rd party utility ) renames the active AFCAD and, for efficiency reasons which would be a bit long to explain here, file renames are not always detected by GSX, so you need to use the "Restart and the rebuild the airport cache" option and be sure GSX is reading the correct AFCAD.
Of course, if the (now correct) AFCAD was never customized for GSX (for example, to add jetways), you will have to configure it again.