Start Command Clarification

When you setup your Start Command, make sure the correct minecraft server JAR file is listed there. The official file is minecraft_server.jar, but when using bukkit, it's something along the lines of craftbukkit-0.0.1-SNAPSHOT.jar.

So the Start command should be something like this for bukkit servers:
java -Xmx1024M -Xms1024M -jar craftbukkit-0.0.1-SNAPSHOT.jar nogui

and this for standard servers
java -Xmx1024M -Xms1024M -jar minecraft_server.jar nogui

This will be much easier/clearer in the next server update.