It's perfectly normal, if you started a GSX customization when you had P3D4, and completed it when moving to P3D5.
The issue here is that, while P3D5 has kept all the .BGL filenames as they were in P3D4, they changed the naming and the position of the gates and, since GSX matches a .BGL with its related .INI file by name, a GSX .INI which was made for P3D4 will be loaded in P3D5 as well ( because the .BGL has the same name ), but some position might not match.
The easiest solution would be removing the GSX .INI file altogether and redo your customizations, we are considering adding an extra parameter to the .INI, to make it "P3D4 only" or "P3D5 only" so, if you want to keep using both simulators, GSX could switch between the two automatically depending which sim is running.