I have had this issue in the past and it never got entirely resloved and now a coworker is having the same issue.
In general I have my workspace set up with my properties/layers/grading/xref windows on my second screen.
When I exit Civil 3D 2013 and start the program up again my windows (usually) all start in the middle of first screen.
I have tried locking floating toolbars/panels and floating windows with no sucess. I have also tried saving my workspace. When I save my workspace if I choose it again after start up sometimes some of the windows will jump to where I saved them.
In addition to start up, everytime I do a grading command the grading window jumps from my second screen to the middle of my first.
Has anyone delt with this before?
I think this may go back to how you Video driver works. In my case I have my full screen AutoCad on Screen No. 1 and let No. 2 have all the "extras". They stay put. The only thing that I have locked is Floating Toolbars/Panels.