Guys thanks a lot for your replies.
As it turns out the problem wasnt with the ie conditional comments but with bad design. To debug this I put a border round everything and worked out what the problem was. I found a way to remove content-container2 and moved the left and right bar into the #center to make it easier to manage. Somehow the redundant container was overridding the statements and only obeying main.css so doing this fixed the issue.
Very weird bug but after spending a hellish week with it im glad its fixed
!