Distorted animations if you dont use Zero Joints Plugin?

I'll make it simple...

I made a model:


I animated it:


and I uploaded it...

It looked like this:


I resaved the .mdx, converted it back to .3ds and opened it.. it was fine, nothing wrong with the animation. Then I bumped into this: http://www.wc3campaigns.com/showthread.php?t=51482, which is a tutorial on creating/animating in milkshape. Here's what it said:

"Before you start animating, you have to run the Zero Joints plugin. If you do not, your animations will not turn out correctly in Warcraft."

Hmm. I didn't do that. The other milkshape tutorial say nothing about it. Could it be that my animation is deformed because I didn't use the plugin? The animation moves like its supposed to, but it is deformed and with the wrong parts in the wrong places. I DO NOT want to animate the model again, so can I open the model back up, then run the plug-in? If not.. does anyone know of a way to make this plug-in convert the joints to the correct format so my model work work correctly.

Note: Tis is my first Wc3 model, and if there is something else I may be doing wrong, please tell me.

im not sure about milkshape since i use 3ds max, although i recomend saving a backup and then use the "zero joints plugin"

I don't think my problem is the Zero Joints Plug-in. I applied it to my animation. All it did was just rotate a few joints. I didn't go to fix them because I wanted to see if that's what the model would look like when I started up Wc3. Well... the model looked just as distorted as before, but the leg was kinda out to the side and his arm was rotated back. Does anyone else who uses Milkshape want to take a look at my model and animations.. and possibly tell me whats wrong with it?