I have added a CSS Generator to the Multi Level Menu page, which should make it easier to get the menu looking how you want.
The error was caused by too many window onload functions since the addition of the User Preference Script.
Since I hadn't actually changed the menu, just added the User Preference Script to every page, I didn't bother to test the menu again in IE.
It would be nice to have an automated testing service that went through your site in multiple browsers and reported what failed or looked wrong and was free.
For now I will have to continue relying on feedback from users and my own testing.
If you see something wrong with this site in your browser of choice let me know as more then likely I have missed it or ignored it hoping it will go away.