Yes. I've said from start that you should change the server files (even KarLi said that in a post from that "fixing GS" thread) xD Also, I think the best thing to do, try to find a 97D server files with source code included. You can add custom things like Party Password joining on whisper, etc.
The website, to check if the GS is online, it will try to ping it and yes, it's gonna send a packet to it which can actually contain a header or something which the GS could interpret it.
Some services can spam your GS port.
Anyway, glad you solved it. Molya xD