Motion Builder - exporting an animation to an .mb
First, load the AnimRef_idle.fbx of the character you want, into Motion Builder, and animate with that.
Before exporting, you have to do this ritual; up on the top right where the picture of the man is, there are some drop down menus... I think you want the one called "Edit". Anyway the option you need to find is "Plot rig" Just click OK on the dialogue box that comes up.
Then click File, export, and it will be a special FBX that only has animation. YOu can tell because the file-type selector says "FBX - Animation only." Save this as an fbx file.
In Maya, open the fbx_import.mb. THen go File, Import, and choose your FBX file. You may need to install the FBX importer plugin. Choose the Merge option on the importer dialogue.
The animation should play correctly and you should be able to save this as walk.mb or whatever animation name you want, and then use the usual Doom 3 export process to get it into Doom 3.