If the skinned mesh is not the root of the b3d, you will have to animate it manually using FindChild(). Whenever possible, you should export skinned characters without checking Scene Root. If you have to add a Scene Root (b3d files with multiple roots are invalid), look at "subanims.bb" in the B3d Extensions library for code that automatically finds animated children and animates them (that's what the B3d Pipeline Viewer uses).
-Pudding
-Pudding