Hey, welcome to the forum.
I am sorry, I cannot help much here. IE6 is a bugger to troubleshoot due to the lack of diagnostic tools. I have come across something similar to this myself recently.
Try applying.
Code:
#nav-element { z-index:20; }
This should set whatever your nav element is above the page. With my problem mentioned above this didn't fix my problem. In the end I solved it by throwing a border around everything on the top of the page. Then setting a fixed height for whatever element was overlapping. Turned out to be a 5 minute job.