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[edited by: tedster at 8:38 am (utc) on Dec. 18, 2007]
[edit reason] switch to example.com - it can never be owned [/edit]
However, it appears to eventually work itself out after a series of shuffling. Our pages seem to be settling with the domain first and then the keyword relevant page indented below. looks to take about 2 - 3 weeks.
I have a six month old retail site with several hundred pages.
So, it's still a fairly new site in Google's eyes.
Most pages doing well in the serps and most of those pages have a page rank of 2 or 3.
That would be expected based on the explanation above. You're just going through the typical "seating" process.
My problem is several pages that are two levels below my home page in navigation have a "unranked" for page rank.
It doesn't matter. PageRank is innaccurate at the Toolbar level. You may see 0 in the TB, but it is possible that page is in the process of being calculated and does have PR assigned, you just won't see it.
They have been crawled as recently as three days ago, other pages on the same level of navigation have a page rank of 1 and 2.
Are the pages without PR newer pages? If so, then what you are seeing is normal.
Click path is what determines how PR is distributed throughout your site. You may need to provide more access points closer to the top of the click path to get PR to flow through to those lower level pages.
Secondly when doing a Google search for the keywords on the unranked pages my homepage ranks #1 but the specific page doesn't appear anywhere. The homepage doesn't have a single relative keyword on it!
Clustering? Google knows about those pages, they just don't have enough juice yet to pull their own weight. It sounds like you are right in that period where the pages are "proving themselves".
My established sites would pretty much follow a pattern say...
Index PR5 the next level PR4, 3rd level PR3 etc.
Not any more
My blog, for example, has seen all it's 2nd, 3rd pages of categories and second level pages of monthly archives all go grey bar as well.
When this happens it effectively removes all the PR from the pages coming off these navigational pages if they are the only links.
The whole PR thing is getting to be a PITA, you have Matt Cutts saying one day don't worry about PR it's not important then somebody says why can't I find a page in Google, answer: it's gone supplemental.
Why's it supplemental Matt
"not enough pagerank" comes the reply!
Although toolbar PageRank is a somewhat rough indicator of real Page Rank, it also can be quite strange, sometimes buggy, and always out of date. It's not worth nearly the amount of focus that people sometimes give it.
Search traffic matters. Rankings produce that traffic, so ranking matters. If pages are ranking and producing good traffic for a website, then it really doesn't matter what the toolbar shows. If there is a ranking or traffic problem, then toolbar PR might give you some clues as to what is going on. Or it might not - as I said, it's sometimes buggy and only a historical picture at best.