The menu, right below the brand, is a sprite menu… for some weird reason, the whole image is being shrinked on IE6, causing a strange "effect"… I don’t know how to fix this, and I’ve seen sprited menus working on IE6…
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If I recall correctly, the filter property doesn’t support background image positioning. That’s probably why the whole image is getting scrunched into place.
It looks like you could use JPEGs rather than PNGs just as easily in your design. Try converting the PNG images to JPEG and then set them through the regular CSS background property. I bet it would work.