Sounds mysterious. In Blender, what I seem to run into most is naming the armatures/emptys/(whatever Milkshape uses as joints and points of interest) wrong, and thus screw up. Also, packaging isn't required. Just put all the required stuff in a folder in add-ons. The only reason you get add-ons as a .zip is because you can't send entire folders.
Milkshape isn't as powerful or reliable as Blender, from my point of view. It just seems complicated at first.
A video!?
Why would i make a video!?
Hurrrrrrrr
Okay, what he meant was that you should show everyone in detail via that (if it just doesn't show up in game, don't). I used Fraps