Webmaster tools doesn't pick up 301 redirect
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I had a few hundred URLs that died on my site. Google Webmaster Tools notified me about the increase in 404 errors. I fixed all of them by 301 redirecting them to the most relevant page and did multiple header checks to ensure that the 301 has been implemented correctly. Now a few weeks later, Google is giving me the exact same message in Google Webmaster Tools but they are all still 301 redirected. WTF?
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You may just be experiencing the delay that happens between crawl time and analysis time in GWT. I haven't seen anything official about this, but in my clients' sites and my own sites it appears to me that it can take as much as a month after a recrawl of a page for Google to respect a 301 or rel=canonical in terms of what it reports in Webmaster Tools (and also what it shows in the search results).
If you've carefully checked the complete set of HTTP responses and only see a single 301, then I would let it site for another 2 weeks and see if the problem goes away. FYI I like to use HTTPfox to check HTTP responses, as I can see the complete chain of responses--not just the last or first in the chain.