Assuming NetWallah didn't nail your problem, here's a few things to try:

• Look at your server's error and access logs. Is there anything interesting there when the problem occurs?
• Turn on IE's Javascript error popup and debugging. They default to off in modern versions of IE.
• Try to boil down the problem to smaller and smaller HTML files that still trigger the behavior. You might find that there's something simple you can change to avoid the problem.
• Post your question somewhere HTML and browser gurus hang out. They know all kinds of things that we don't. No, I don't know where they hang out.

-sam