I had this issue with a website that was built with DNN where the navigation menu stayed hidden behind an iframe on internet explorer.
After a short search on the net, I found the problem was due to how IE processed windowed and windowless elements. Jordan Gray's answer here explained the reasoning behind this problem.
However, even after this, I still had the issue because the dnn navigation menu used an un-ordered list and it wasn't immediately clear to me that I had to place an iframe after every list item.
So after struggling with this for awhile, I finally figured it out and I wanted to share it so it may benefit someone dealing with the same issue.