I’m not sure, but this sounds like a javascript thing. I don’t think I can help, but if you post a link or screenshot it might help others understand better what you are looking for.
In the mean time, I’d try looking for a javascript menu plugin or other custom menu plugin for wordpress.
Have you considered re-organizing your menus to have more division or sub-groups to reduce list size? How usable is a menu that runs longer than the screen?