I just ran a test on a template I had, The Clean Up XHTML command did not have an adverse affect on how it displayed, but the Clean Up Word HTML command did.
The report said: "removed 3 word Ifs.."
What it actually removed where 3 conditional css rules:
1:
<!--[if IE 5]>
<style type="text/css">
#outerWrapper #contentWrapper #leftColumn1 {
width: 175px;
}
</style>
<![endif]-->
2:
<!--[if IE]>
<style type="text/css">
#outerWrapper #contentWrapper, #outerWrapper #contentWrapper #content {
zoom: 1;
}
</style>
<![endif]-->
3:
<!--[if lte IE 6]>
<style type="text/css" media="all">
@import url("../CSSMenuWriter/cssmw_content/menu_ie.css");
</style>
<![endif]-->
these conditional css rules are used to fix bugs in the way IE renders CSS. When I tested the page in the browser, it displayed fine in FireFox and in IE7, IE6 however, the menu did not function because the CSS Style sheet needed to display the menu in IE was not attached, that was the third conditional CSS block that was removed.
The Clean up Word HTML Command is mistakenly detecting the conditional css rules as word specific markup. You should not have a problem with the Clean Up XHTML Command, but I would avoid the Clean Up Word HTML command.