Please don't take me as the last word on this but the problem as i understand it is that Microsoft, when developing IE, decided the W3 rules on CSS behaviors was not interpreted correctly by the rest of civilization. As a result, IE treats things like margins and paddings differently than Firefox would. Or maybe it's just padding or just margins- i can't remember.
I ran into this problem as well. I settled on a theme i liked that played nice with both browsers. As a personal side, i don't really care how it renders in IE since i find Firefox a much better browser. Of course, your mileage may vary.
Look at your blog via Firefox and see if it renders better.
best of luck,