I'm having the same problem that is in this topic: http://www.minecraftforge.net/forum/index.php?topic=1476.0
Server is using Forge 4.1.1.251 and I'm starting the server with "nogui". Console shows nothing when trying to use a command like help.
ForgeModLoader-server-0.log, server.log and the server GUI that shows up without "nogui" do show the help list properly.
I didn't have this problem with Forge 3 for 1.2.5
ForgeModLoader-server-0.log: