Hmm, here, lemme list the steps I took to make it work correctly
1. I downloaded your file, proto_rigged_3.blend, and opened it with Blender 2.49b
2. I selected the mesh in Object Mode and under the Editing Panel, I deleted the armature modifier, and then deleted each vertex group on the object by spamming the Delete button in the Vertex Groups section of the Link and Materials box. This is important to erase any trace of the previous weighting.
3. With the mesh still selected, I Shift+Selected the armature (any bone in the armature) so that both the mesh and the armature were selected (armature must be selected last) and hit CTRL+P to parent the mesh to the armature using Bone Heat.
4. Then I just exported the model with Include Frame Rate, Export Armatures, either Keyframes or Full Animation, and All Objects.
5. The exported model loaded and played in the DirectX viewer, and in DBPro (I dunno about DGDK, but I can imagine they'd behave the same).
I hope that helps. Let me know if you still have questions.