Scoble says that the Radio trackback feature (which is implemented identically to the Manila implementation on this site) makes his site fail validation. Frustrating when a useful feature like that has to be turned off, but I understand the pain; I’ve been working on validation myself.
At this point there are still a bunch of errors reported by the W3C’s validator, none of which I can do anything about. They all have to do with ampersands in URLs in my articles. Ampersands are commonly used in URLs when there are multiple arguments. Manila thinks that those ampersands should be represented by actual & characters (and enforces this in its managed content), while the W3C validator insists that, at least for HTML 4.01 Transitional, the ampersands must be represented as &, even in URLs. So there’s nothing I can do; the site is as valid as it’s going to get.
(Incidentally, if anyone has Manila spitting out valid XHTML, I’d love to know. It would be nice to get off HTML 4.01.)
For more info about CMSes and HTML validation, there’s a great interview with What Do I Know’s Todd Dominey over at WebStandards.org.