Indexed...but not indexed. WTF?

Here is a weird one.

I set up a cluster of new sites about a month ago. They are all in different niches, but the structure and format for each sites is almost identical....only the content differs.

One site got indexed by Google right away, and is now rocking away, with Google traffic increasing daily...awesome!

But it's a different story with the other six. Google Webmaster Tools shows that they have all been indexed, most have lots of URLs in Google, and Google has analyzed the pages and worked what the main keywords are. It also says that some are getting impressions and clicks in search.

Yet when I do a site:domain.com search for any of these domains, Google brings back:

"Your search - site:domain.com - did not match any documents."

Also, if I copy a sentence from the home page and Google it in quotes, I get zero results.

So the sites are indexed...but they are not indexed...

How does that make sense? And more importantly, what can I do about it?

Keep gradually link building at a somewhat passive rate and give it time, this happens to my sites as well.

maybe try changing the layout of the all of the sites if they're all the same

A friend of mine had a similar problem recently. His keyword density was too high. He cleaned it up and the site was indexed (at least for site:domain.com query) within 24 hours. However, I think it gave him a penalty because he's not showing up in any keyword queries at all, despite having an optimized domain name + content. I would expect if this is the case the penalty rolls off after a month or 2.

have you tried site:www.yoursite. com ?