I never found a solution online, so apparently this is a problem that still exists and is unsolved. I was dumbfounded when I tried to switch one of my Minecraft servers over to Ubuntu Server x64 from its previous Windows operating system. How could nothing much change in the server software, and have it fall flat on it’s face, seemingly with a crippling bug?

After many hours of working on this issue, I have come to the proper solution. The issue is the server computer’s MTU size on the Ethernet interface. In my case, the Windows box was fine, but the MTU on my new Ubuntu Server needed changed.

I changed the MTU of my Ubuntu Server to 1492 from 1500, and magically it worked. Users were not stuck at “Downloading Terrain” or had their login hang until a “Socket Error” occurred.

To do this fix on a Ubuntu Server (or possibly other linux distro), simply run the command

sudo ifconfig eth0 mtu 1492

(You can subsitute “eth0” for your interface card/number, and the “1492” for whatever MTU size you need to get your connection working. Mine was 1500 and failed, 1492 was the key to get mine working. This may or may not be the same for you.)

Your issue should now be fixed! But that fix won’t survive a reboot! You’ll need to either run that command at boot automatically or manually. To make a fix that activates at boot, you’ll need to edit your /etc/network/interfaces file. To do this run this command:

sudo nano /etc/network/interfaces

Then in the first stanza, for eth0 (or whatever your network interface is), change it to add “mtu 1492″. (In this method, the interface must be set to a static address, but you can find ways to set the MTU of a DHCP interface online elsewhere.)

...
iface eth0 inet static
     address 192.168.0.2
     netmask 255.255.255.0
     gateway 192.168.0.1
     mtu 1492
...

You can now either reboot the system, or restart networking (sudo /etc/init.d/networking restart) and your fix will live on past the shutdown.

For Windows users, the fix is usually a registry edit (there is also a command available to set the MTU of an interface elsewhere):

Start > Run> REGEDIT.exe

Go to : 
HKLM\System\CurrentControlSet\Services\Tcpip\Parameters\Interfaces

 Select the Interface you want to fix, for example
interface value: {111112-2222222-666666-777777}

Right Click on Right Side and create a new RegWord type with:

      Name: MTU

      Value: 1492

      Type: Decimal

 Restart the System

This is a great tool for minimizing Folding@Home console clients to be out of sight and completely out of the way. Do remember this is an early version, and while it works, it doesnt have all the features yet, just the basics.

Download TrayInjector here (363kb, v0.1).