Typing any commands shutdown server ** Help **

I am using the latest build of CraftBukkit on my Ubuntu server.

When I run the server it loads fine and I can enter the world, but when I type any commands it shuts down the server completely.

It shuts down when I type any command or when I type / or /# or !#.
Could someone tell me a solution or what I am doing wrong?

I also have a few plugins that it apparently doesn't load at all, I see this is also a problem with Bukkit.