You might be suffering from FOUC. (Flash Of Unstyled Content) whereby IE6 for whatever reason isn't rendering your content correctly on the first load. (we would need to see sample code or a URL to determine why)
The 2nd - Nth reloads may work well once some of the content is cached by the browser.
updates
Ok, now seeing the site a few more details. The div that loads the new content is floated over an animated flash background... and the divs appear to use a png image background with transparency (IE6 doesn't support PNG Alpha (the part that does transparency)) thus IE loads an ugly image first, and then it looks like you have a hook in there to swap it out with a filter in IE. (I'm kind of guessing at the moment as the PC I'm on with IE6 is rather slow and the flash appears to be very cpu intensive)
Since this PC is slow, I see the text/form content load before the background image... I'm wondering (if you are applying a filter in IE6, if that is being executed before the image is fully loaded and thus the end result looks odd) but due to browser caching, the 2nd/Nth loads are ok?
I need to dig a bit deeper, but I don't have all the tools I need here. Hopefully later today I can check this out a bit more (or someone else will)