I have a small Tool Pallet for my drawing work and have the layer, propertie en content pallet minimized against the top. So I always have them at reach when needed. I Do not dock, because I work on macbook pro and then have more screen space. But whenever I reopen autocad, those pallett are all over the screen and even the layer one, always seem to dissaper completely..
I have experienced a similar problem, however only when changing display resolution or if using AutoCAD on my 15" Macbook Pro and then connecting to my 27" Cinema Display. This is not unique to AutoCAD however as it relates to window positioning at different display resolutions.