What is most likely happening is that those objects are mirrored objects and you have frozen the transforms on them which sets the opposite attribute, you can turn this off in the shape node of the object by unchecking Double Sided and then uncheck the opposite attribute and finally rechecking the Double sided.
Another possibility is you are getting a double transform somewhere , it might help to group those objects to themselves to freeze out the transforms.
The eyes would be better off being parented to the head joint rather than being bound anyway, as for the hair is it on a skull cap or attatched directly to the head geo ?
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