Strange Rigging Glitch

I have this scene where a character is in the middle of the sea in a box. The mesh of the character is rigged with Armatures which is parented to the box which is parented via vertex of the sea which is moving. Whew. Now my problem is this: The Characters arms and head move in ackward swaying motions, and are not moving relevent to the rest of the body. Here is a sample Animation from my website (2mb):

As you can see I also posted what my rigging looks like. I know I should use Joint Handles but I am lazy. So what should I do to get rid of that weird moving? Any suggestions?

Can’t look at the movie for now, I’m on linux. But by what you say, I would sugest you to tcheck for the bones that are moving: Are they parented to the rest of the armature? are they ik target? etc…
All root of chain, or bone if they are alone, should be in a way parented to a root bone which don’t move so if you move the armature object, this bone will always stay at the “relative” same place.