When I duplicate a sublayer, then move that sublayer out of the layer it is a sublayer of, the positioning of all the content is shifted, but the positioning of all the content of the layer remains the same in relation to each other.

This means to get a layer which is EXACTLY the same as another, position and all, rather than duplicating and moving the layer, I have to create a new layer, then copy and paste to that new layer. This becomes very problematic when you want to copy a sublayer and it has lots of its own sublayers. You would have to manually create the layer and all its sublayer structure, then copy and paste to each layer!

Help! Is this happening to anybody else? What's going on?

I have Windows 7 64bit and Inkscape 0.91 64 bit

Hello
I don't understand what is your problem, or what are you trying to achieve. Just saying: a layer, and a sublayer are just special kind of groups.

Could you post a sample file?

Known issue:

• Bug #1194091 “rearranging Layers may shift object location”

Will be addressed in the next major release (0.92).