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For a given search phrase, an inner page with hardly any BLís is the first page from a site that appears in the SERP's, and the homepage is nowhere to be seen.
This is despite the fact that the homepage is targetted for the KW in question, and has far more 'anchor texted' BLís.
An example to illustrate:
www.abcdef.com sells widgets.
The homepage ranks first for 'abcdef'.
The homepage previously ranked well for 'widgets', and has many BL's with 'widgets' as anchor text.
Now, the homepage does not show up in the SERP's for 'widgets', but an inner page, call it 'www.abcdef.com/specs.html' with a title of 'List of widget specifications' shows up in position 98 for 'widgets'.
In one example that I am aware of, the inner page which does appear in the SERP's for a search phrase has NO external backlinks.
It does not have the characteristics of a 'penalty' situation. The PR is unchanged, the homepage shows up in the 'site:www.domain.com' results, and shows up first in SERP's for a search on the site name.
From previous reading, it doesn't seem to indicate a penalty, so a re-inclusion request is not appropriate. I am at a loss to know how to resolve it.
My personal opinion is that it appears to be some sort of 're-sandboxing', but this is just an opinion.
I and two other visitors to Matt Cutts' blog raised this issue in comments to a post. He has not discussed the particular issue (yet), so I thought I would post it here. Hopefully GoogleGuy might see it and tell us what it indicates.
Look at your homepage and the deeper page and see if you can find any on page items that could have affected the placement.
But then you might want to wait till the update is over to be sure what you are seeing now is permanent.
Thanks for your advice. Certainly I'm not worried about PR - I just mentioned it to illustrate that this particular situation din't have the characteristics of an exclusion, where PR is reduced to zero for an offending site.
It will be interesting to see if Jagger 3 does anything to resolve the issue. I'd still like to know what caused it to happen in the first place, though...
I doubt it's a penalty and at present hanging fire until this whole jagger thing is over.
I tend to believe its an indexing problem that occured with Jagger1, what i was surprised at was the way in which GG and Matt after a couple of days then said there are two more updates on the way. I don't think that these two further updates where anticipated but more along the lines that Jagger1 didn't really produce the effective results that they where after.
Apart from one for the homepage, the rest were for pages on a PHPBB2 forum within the site - PHPBB2 may be written using relative links in the code, and this might be part of the problem.