Unfortunately Removing the duplicate Right Arm and Left Arm, and the Extra Right Arm.001 and Left Arm.001 did not change the animation at all, I was really hoping it was going to be that simple of a fix.

EDIT: It has to do something with the SMD format, I exported to .dmx and the animation works fine, unfortunately I can't use .dmx, and I really need .smd

EDIT2: I exported to dmx and exported the dmx to smd and it worked o.O so problem solved?

Dropbox link to .Blend File[www.dropbox.com]
If anyone minds taking a look at it and finding out why it exports to .smd so oddly, i'd really appreciate it <3

EDIT: I have not used any bone scaling at all

Why does my animation in Blender export to .smd with it's weights not how I set them? Example[gyazo.com] I know I must be doing something wrong, or some setting is off.