Simple as that is, that's a nice bit of rigging you've got there you know. Anywho I loaded this up into 2.56a had a look and then just exported it as is. To check the animation I loaded it up into the MD5 model viewer and couldn't see any of the nasty wobbling shown in the video. The only reason I can think it *may* do that is because you've not keyframed strategic points along the timeline - it's been my experience that Blender has always had issues with cyclical sequences that you often have to keyframe around to force proper rotations.
[EDIT] split topic and moved to content section.