I have changed the server name (using both motd and server-name in server properties) but it never refreshes on the GT page, even after multiple scans. I have changed the name a few hours ago, the vote sites see the change but GT doesnt. How long does it take to update?

After the server name is changed, it will take effect the next scan. You can even click the Claim Ownership button prior to the page actually showing the name if you have already changed it.

You'll need to make sure to restart the server after making the change.

If you are referring to http://www.gametracker.com/server_info/198.12.80.232:25565/
It is correctly reporting the name being returned from the server "---=[Chromatic-Craft - Survival and Skyblock]=--- ". I've confirmed this at other scanners as well.

The image banners may take up to an hour to refresh the name on it, though.

Yup, I am referring to that server. The thing is, the name is actually now "[Chromatic-Craft - Survival and Skyblock]" without the ---=/=---. You can check via the MC client or a vote site like this one: http://mineservers.com/server/12764/view/chromatic-craft
here the name is correctly scanned.

I'm still seeing that your server is returning the name with the ---=. I have confirmed that Minecraftviewer and a couple others are showing the ----= as well.

Have you restarted the server?

Can you post a copy of the server properties with sensitive information censored or removed?

#Minecraft server properties
#Thu May 29 08:25:24 GMT 2014
generator-settings=
allow-nether=true
level-name=world
enable-query=true
allow-flight=false
server-port=25565
query.port=25565
level-type=DEFAULT
enable-rcon=false
force-gamemode=false
level-seed=
server-ip=198.12.80.232
max-build-height=256
spawn-npcs=true
white-list=false
debug=false
spawn-animals=true
hardcore=false
snooper-enabled=true
texture-pack=
online-mode=false
server-id=unnamed
pvp=false
difficulty=1
enable-command-block=false
server-name=GameTrackerClaimServer
gamemode=0
max-players=30
spawn-monsters=true
generate-structures=true
view-distance=7
spawn-protection=0
motd=\u00A76[\u00A7cChromatic-Craft - Survival and Skyblock\u00A76]

And yes, I have reloaded my server. What I see when using the MC client:

You seem to have the name setup correctly for the MOTD. I'm not familiar with the coloring, but I assume that is correct.

You may want to try updating your server, since it is quite out-of-date.

You may also consider removing plugins that you think might have an impact.

I just compared the standard gamespy4 vs the old minequery query responses and get the similar results:

GS4: ---=[Chromatic-Craft - Survival and Skyblock]=---
Minequery: ---%3D%5BChromatic-Craft%20-%20Survival%20and%20Skyblock%5D%3D---

If the "vote" websites are using a non-standard query protocol or filtering the name, they could very well have different results.

Looks like you were able to find the issue; if you don't mind, may I ask what the cause was?

It seems there is a real difference between /reload and a full restart.

Using /reload, the MC Client and some sites see the new MOTD
A full restart is seen by GT/MCV etc.

Probably a weird cache issue within MC

Thanks for your help. I will have to wait for a quiet period to change the motd and restart the server twice to claim and redo the motd.

Its a little strange though, there are plugins to allow you to change the motd dynamically, those dont restart the server and should be seen by GT or?

Interesting. I don't know enough about running a server to know muhc about /reload. Though, typically communication between "master servers" and your server vs external scanners and your server are a bit different. I would suspect there would be a bug with the plugin that allows you to do that, or possibly some cache issue like you suggest.