That is why I have yet to d/l sp2. I still hear about bugs in it and was just surfing the ms page where the d/l is ,and see they are specific that conflicts or probs can occur and one must follow their directions to a T.It does not seem to promise no probs if all is followed, hence; I am scared of it. I assume you have thought of reinstalling the IE copy? I hope the ms page ,which can be found from a link on this site, can help you.
I am sorry I can't think right now what would be refreshing the IE. I would track down what operation works the IE and look in the folder. See if you can find the root of what operation controls that,( would a wrong key or code in registry be throwing the timing off or hold?) or maybe just get rid of it and install a new copy after saving your bookmarks etc.
Good luck.