One thing I notice is that you have no container the divs just all float on their own. That isn't causing your issue but I dunno, I just find things easier to control if I work with containers.
I think (I'm still relatively new to CSS too) if you float both columns left, then clear the floats after the last column that might fix it. To be honest you do things a lot differently than me, I always use fixed sizes rather than percentages just because it's easier to see how it's going to work on any machine and you never get these issues. I design generally for 1024x768 which means a 955px main container for me anyways, this means it looks fine on any screen. Even widescreens look okay although the side bars are a touch wide.
If I were you I'd search Google for "CSS Box model" & "CSS float layouts" and read as much as you can till you have a handle on how it works.
Good luck, sorry I couldn't give you a specific answer.