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I have submitted simple text sitemap to Google Webmaster tools and after few days it was crawled, after few more most links were indexed according to GWT but it is not showing those links in google. If I do this search (site:domain.com) I only get few url's instead of a few hundred. Is there a delay between GWT showing that pages are indexed and those pages showing up in search results?

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In the end it seems that it was just a delay in Google index updating. Since now over 100 links are indexed properly I don't think there were other issues. –  DominicM Jan 23 '13 at 0:23
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up vote 4 down vote accepted

Google may crawl your page, and show it in GWT, but still not bother showing your pages on the SERP page.

This will, for instance, happen if Google think that your site is without interesting or original content, or if Google think you're doing black-hat SEO.

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I understand that crawling is not same as indexing but why does GWT state that pages are INDEXED when they are not? it it just a flaw/bug in GWT? –  DominicM Jan 20 '13 at 17:44
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If GWT state the pages are indexed, they are indexed. Having pages indexed is no guarantee for them showing up on the SERP. Google is eager to to please. If Google don't think your page will please Google's audience, then Google will not link to it. –  Svartepjotr Jan 20 '13 at 17:51
    
That makes sense. An odd thing is that the one url I submitted via GWT manually is showing up in SERP but the others that were submitted only via a sitemap are not showing in SERP even though they are comprised of equally duplicate content. Any thoughts as to why? –  DominicM Jan 20 '13 at 17:56
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@DominicM: "duplicate content"?! Google is going to avoid showing duplicate content in the SERPs - this might be your problem. Do you see the message in SERPs: "In order to show you the most relevant results, we have omitted some entries very similar to the XXX already displayed."? Otherwise if pages are classified as "indexed" in GWT then they should appear in the SERPs if you do site: search? –  w3d Jan 20 '13 at 18:07
    
By duplicate I mean aggregate (not duplicate on my own domain). Yes, I do see the message though that might be because there is one url with "/" and one without and thats the only url that is added after clicking the "repeat serarch with..." –  DominicM Jan 20 '13 at 18:14
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