I found that using the HTML Tidy for HTML minification broke all my IE rendering. Using the "Default" built in minify options resolved my IE problems. I noticed that HTML Tidy was actually purging some of the comments-in-code. Even with HTML Tidy selected, and unchecking the comment functions it broke IE (though I could not tell what the root cause was from view source in this particular setup). Bottom line is that I could not make W3TC work with HTML Tidy selected, and minification enabled.
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