If you have not added the server, you just need to enter the correct query port on the add server form.

If it is showing as down, update it from the "manage" page (or click "claim server").

I wasn't the one that added the server the first time.
When I try adding the server with the correct query port I receive a message that says
"A server with this ip/query_port already exists in the GameTracker database."

This is my server http://www.gametracker.com/server_info/203.98.81.235:25565/
Address: 203.98.81.235 Port: 25565

It will not let me change the query port no matter what.
Are you by any chance able to change the query port? to 25565?

Check it out at http://www.gametracker.com/server_info/203.98.81.235:25565/

Thank you so much burn!

I added my Minecraft server to gametracker last night and this is how I got it to work.
in the server.properties file I set,
enable-query=true
server-port=25565
query.port=25566
server-ip=192.168.1.16
motd=gametracker
After it's added to Gametracker you can change the MOTD back to your server name and restart the server again.

In my firewall (Linux gateway sever) I set 2 ports forwarded.
port 25565 TCP game joining port.
port 25566 UPD query port that gametracker will use.
Then I reinitialized the firewall.
If you are useing a normal modem/router then you just "apply changes" or "save changes" or reboot it depanding on how your router works.

Things to look out for: The query port forwared has to be UPD. When I tried TCP it would not work.
Any port number will do, the port number dosen't matter, what dose matter is that the query port number in your server.properties file and in your port forward setting (in your router) and the port you type into Gametracker to query your server, are ALL THE SAME PORT NUMBER, I used port 25566.
Other things to check is that your server has a static local ip set, e.g. I set mine to 192.168.1.16. the IP in the server.properties must match your local server IP. Do not confuse this with you WAN IP (IP from the internet). If your not sure how to check your local server IP or how to set it, google it, it's very easy.

I hope this helps