Sounds to me like Double transformation ..

Make sure your skin is NOT grouped OR parented with the skeleton, and at the same time being used as a skin ..

Outliner example :

POLYGON_SKIN
[+]Skeleton

if you need certain parts of your object to follow a bone exactly, then dont bind it as a skin, but parent the object instead.

Outliner Example:

POLYGON_SKIN
[-]Skeleton_1
[-]Skeleton_2
POLYGON_OBJECT (not bound as skin - only parented)


I hope it helps..