If you install KatMouse (http://ehiti.de/katmouse/) it boosts Windows' scrolling functionality so you can scroll background windows without giving them the focus or bringing them to the front. (Like Mac OS X supports). Not a fight, just a must-have accessory.
Something else that perplexes me is that even when a window has focus sometimes it still won't scroll. Doesn't matter how many times I click on it. But if I go to the sidebar and jiggle that, it gains the ability to respond to the scroll wheel again. Odd.