Acrobat Reader- How to open the same document in separate windows?
I do not know, how Adobe Reader 9.4.6 behaves, but in the current Acrobat Reader X (10.1.4 in my case) there is an option exactly for this case:
(i am translating from a localized version, so menu names can differ)
Menu -> "Window" (the one next to Help) -> "New Window"
And voila, you have multiple windows with the same document. The windows can be distinguished by the number behind the filename eg. filename.pdf:1, filename.pdf:2, ... filename.pdf:n