so I run the control panel and I restart the sim and I get the same message again...
You shouldn't just run the Control Panel and restart the sim. As the message says, you must allow it to re-patch the default jetways to exclude them so, just click the "Disable Default Jetways" option, and the message will go away.
The reason for this message is that, after a simulator update, the default scenery (which was patched to remove default jetways by the GSX installer) will revert to the original unpatched version so, if GSX didn't checked, you would see double jetways (default+GSX) so, instead of creating double jetways and left you wondering what to do, it gives that message, so you know you'll have to patch the default jetways again to remove them, with the GSX Control Panel.