I have a similar issue with Millenaire 3.1.2 running on a fresh 1.3.2 server. I added FML 4.0.0.241 and added the Millenaire folders to the mod folder inside my server folder and boot up my server and it starts, also fresh 1.3.2 client with the same FML and the client Millenaire 3.1.2 added in it's mod folders. now i can run the client and play with Milenaire just fine in single player mode but when i try to access my server it gives me a warning that I am missing Millenaire on my client and refuses my connection.