It's funny how I see a lot of blame placed on IE but the same exact problem appears in Firefox, Opera, or whatever browser I use to view/reply posts.
I wrote a function to re-format the quote tags directly from the database and that worked for new replies but not for old ones already in the DB. My function just moved the /quote to be in order, so quotes show in order as individual boxes, not nested ones.
The problem is incorrect ordering of /quote tags in the DB - it has nothing at all to do with browsers. I wish it was as simple as IE, then I could just detect IE and serve modified content.
I'm thinking about using that function and writing another to update old replies so it finally works...