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Please compare http://validator.w3.org/check?uri=http%3A%2F%2Fwww.w3.org%2F&charset=%28detect+automatically%29&doctype=Inline&ss=1&group=0&user- agent=W3C_Validator%2F1.2 (works) vs. http://validator.w3.org/check/?uri=http%3A%2F%2Fwww.w3.org%2F&charset=%28detect+automatically%29&doctype=Inline&ss=1&group=0&user-agent=W3C_Validator%2F1.2 (broken). I think the problem lies in <style type="text/css" media="all">@import "./style/base"; @import "./style/results";</style> which leads to /style/results in the first and /check/style/results (404) in the second example. This probably also breaks some other include paths but I didn't check. The second example definitely used to work as I have a bookmark that leads to the validation results that broke a few months ago. Took me until now to look into this (and hopefully figure out what's wrong).
/check/ was never really meant to work, I suppose it just happened to work as a side effect of the /check/referer functionality which was recently removed after being deprecated for ?uri=referer since 2003. There is still a backwards compatibility /check/referer handler in validator's front-end, however IIUC it just handles /check/referer, not /check/.