I would check the site's CSS with
the W3C CSS Validator and the HTML of your produced page (not template!) with their
HTML Validator. Since these guys set the standards, your code should adhere to the validations, which work pretty smoothly.
I'm assuming that if there are IE6 bugs that deviate from the HTML 4.x doctype standard, that these issues would be on Microsoft's support area (maybe).
You'll want to let them look at your style sheet template as well (you may have to make it into a standalone file for their purposes - copy/paste the code out of your template editor and save as a .css file).
Also, I had a lot of trouble tracking all the myriad nested div's in some of these templates, and noticed that I had left some unclosed. The validators can pick that up as well.