Ok, let's get the obvious out of the way;

- Running Bukkit.
- Bukkit config has scanning active.
- Bukkit config has port properly setup.
- Router is properly setup to forward the port.
- No traffic blocker (firewall/antivirus/antispyware) on server.
- Gametracker can scan the port (when it decides it wants to)
- Server has no hibernation mode.

Occasionally, and for no reason, Gametracker will display my server as being "Dead". Even if I try to update the port (without changing the number) it still reports that it's unable to scan the server. I will admit that I do have some Bukkit plugins, just like every other server in existence. That said, I'm not running anything that would interfere with Gametracker. It's just standard Bukkit with normal things like PermissionsEX, Dynmap, Residence, and Protection Stones.

Any idea what's wrong? Pretty sure the issue isn't on my end considering GT can occasionally detect the server, without me changing anything on my end.

Perhaps GT should consider going back to a server-side bukkit plugin to gather our server information, instead of relying on scanning the server across the internet. I'd volunteer to install a (version compatable) plugin for my bukkit if one was actually available.

Creating a server plugin, which GT has never done, would cause a lot more headaches than it would be worth. It is a lot easier on both ends just to use the built in query protocol.

Your server has some sort of anti-flood measures in place, which is preventing GameTracker from getting a response from subsequent scans until it is "unblocked." This is my best guess based on scanning it successfully once, then getting no response repeatedly.

Good luck.