For IE6, one thing I noticed was the widths on the menu's have been changed to "auto". That is probably why the menus are taking the entire width. Defining a width should fix that problem.
For IE7, its a little harder to say. It could be the "height: auto". In general, you shouldn't have to give a height value since the text, padding, and margin will give you the necessary height.
My recommendation to troubleshoot is start with a preset and your menu content, then just verify that is working for you as a base line. Then do small changes to the design and test it out. That should allow you to figure out which properties are causing the issues. My initial guess is the auto width and height's being the issue.