I can't reproduce this, made this simple test:
- Put all services to Disabled, Apply
- Selected a single airport (KCLT), set it to Enable, Apply
- Went back to the first page, performed an Update CHECK
- Back in the Config page again, KCLT is still Enabled, everything else is Disabled.
- Restarted the installer, KCLT is still Enabled.
Could be the 3rd party airports you are enabling have their own Airport Service files ? In that case, it's perfectly normal they would be disabled again during an update, because the update does exactly what the "Exclude 3rd party" button would do: excludes all 3rd party airports from GSX jetway replacement and, if they have their own Airport Service files, exclude the services as well.