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When I try to validate a page, say http://www.gm.ca/gm/english/corporate/about/ourcompany/overview through the URI tabbed interface, I'll see an error relating to not finding the doctype. However, if I copy the source directly and validate by direct input, I'll see different errors completely. Should these not be the same exactly?
If given the exact same input, then yes. But in practice they're never exactly the same, there are server generated headers and possible content negotiation in the equation when validating by URI etc. In this case, I bet the document served to the validator by the www.gm.ca server is pretty far from the one you're feeding it with direct input; use the "show source" option to see what the validator received.