Sorry for the late reply after my initial postings. I'll try to answer all the questions that have come up:
I have tried this with both a fresh install of 5.0 and an upgrade over a 4.9 install. Both had the problem. This was tried on a Windows 2000 and Windows XP machine, both physical and virtual, neither had the "multiple IE" install package. They were running "real" copies of IE6.
Caching, cookies had been cleared, IIS had been reset after install "just in case", nothing regarding privacy settings are a problem; this is an internal site (Trusted Intranet) but double-checked anyway and it was fine.
As Jon mentioned, the problem was not prevalent unless I was logged in. In other words, as an anonymous user it was just fine but the moment I logged in then the problem occurred. Also as Jon mentioned, everything towards the top half of the page was dead, then near the bottom things were magically working.
@Jon -- I'll have to try that in the default.css file, that is removing that line in the ModuleTitle_SubMenu class and seeing what happens. I'll post back as soon as I look.