If you use Macromedia Dreamweaver to do ASP.NET development like I do, do not attempt to use XHTML. The ASP.NET controls don’t play nice with XHTML validation unless you do a bunch of subclassing to enable compatibility, as Kevin Brown describes in his excellent article.
Suuuure wish I’d known this before I attempted to convert my project to XHTML. Fortunately because of Dreamweaver’s righteous templating features, it wasn’t difficult to undo the my errant attempt at XHTMLization. Interestingly, Mozilla will do its best to display a page that’s marked as XHTML-compliant but isn’t really, while IE6 barfs if you get the slightest thing wrong. This is an interesting and unfortunate turnabout from the old days when IE would display poorly-formed tables that would make Netscape 4.x bite the dust. One more bit of evidence that Mozilla is the better browser.
I guess that now that they’ve announced the product and released to manufacturing it’s OK to mention that I was on the Dreamweaver MX 2004 beta. My two-sentence review: lots of goodies if you use CSS. Not much there besides bug fixes if you’re using ASP.NET. I’ll still upgrade though; nothing else touches Dreamweaver for Web UI development. Still.
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I like using text editors like jEdit to edit XHTML content directly still. I am finding that by using a modern DIV layout with CSS I have a great deal of control over the pages. But I would still suffer the same problem you describe. If I use syntax that Visual Studio does not like I will have problems. And I am not sure how well Dreamweaver handles DIV+CSS layouts these days. The last I looked it was still largely tried to table layouts.