I can't replicate this problem and, I created a very complex profile with everything customized very recently, and I couldn't find any issues with saving the profile.
I had same experience when I worked on one very difficult custom airport: every parking spots are with different numbers and places, I all correct that
This already seems to indicate a problem even BEFORE you started customizing the scenery. If all parking spots are "wrong", it seems GSX hasn't loaded the correct airport for the scenery you are using, but this changes a lot depending if you use the SU10 Navdata option or not.
As indicated in the manual, when the SU10 Navdata is Enabled, GSX no longer knows which .BGL you are in: it just ask for the airport data using Simconnect, so it will be your responsibility to be sure the GSX airport profile matches the airport used.
If the SU Navdata option is Disabled, instead, GSX will need to load the scenery .BGL so, it might have failed to do so for some reason, like the file too big, a problem with reading the file, or just because the scenery is bought from the Marketplace, so GSX can't read it, and it's reading the default airport instead.
Please make a precise report about where and how this happens, providing precise, exact, details on the scenery used and what the airport customization page is telling, and if the SU10 Navdata option is used.