application windows in mountain lion

Hello,

I installed Mountain Lion on my 2010 MacBook Pro a few weeks ago. Since doing so, the following is happening: I have 2 Word documents open and another app ('R') open as well. When I click on one word document, both word documents move to the front.

Ideally, I'd like to be able to have the Word documents open (side-by-side) and the R window open on top of one of the Word documents. This way, I can refer to the Word document assignment as I program code in R. However, this seems to be impossible in Mountain Lion!

Is there some way to