QUOTE (Nightowl @ Sep 24 2008, 05:52 PM)

"Cleaner Resetting order of IE Favorites/Bookmarks? How do I disable that?" found in search, I tested many variations, uncheck Window Size/Location Cache seem to work so far

I don't recommend using the advanced section unless you have a specific need.
I have one custom folder that I empty now and then.
None of the cashe cleaning items
should be changing the order of your favorites.
I did some forum searches and see that this can happen, but I don't think its CCleaners fault.
To state the obvious, I would leave Window Size/Location Cache unchecked.
Have you thought of updating to IE7?