Hi Jared, I have not been able to reproduce this problem at all so it's hard to give any decent advice. The thread you linked to shows that Noobert's problem was resolved and his issue turned out to be other CSS on the page interfering with the menu.
Quote from that thread: "Aha! I found the problem. It has nothing to do with your excellent plugin. There was a z-index issue with some of the absolutely positioned elements on the page. My mistake." If this was a Superfish bug then I would think that the vertical example: http://users.tpg.com.au/j_birch/plugins/superfish/vertical-example/ ...would suffer from it as there are four levels of menu there, but it works perfectly for me in IE6 and IE7. Do you have a link we could look at so we can investigate further and get to the bottom of the matter in your case? Joel Birch.