If the examples that come with Blender's .b3d exporter work then you aren't setting up your models correctly from within Blender. Compare the "Outliner" window with an example file to your file. The structure should be the same (Mesh armature action etc)
Does the animation play correctly from within Blender?
The exporter does work perfectly.
Does the animation play correctly from within Blender?
The exporter does work perfectly.