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Many of those subdirectories are being dropped from the G-Index while the home page and pages in the main directory are doing just fine.
Is it possible G is starting to consider external links to subdirectories important? Or that G wants more than one link on a site to consider subdirectories important?
-s-
In the travel sector I saw one very nice and professional site drop off the face of the Earth for probably 400 money-searches. They used a different domain name for each city name but all domains came off the same IP.
Conversely, I saw another HUGE site gain dramatically in rank for numerous $$$ searches. It uses subs for each city name, and it's built mostly on internal links, so I can't really see a pattern between subs and external links, but this site does have 300-400+ internal links to most of its subs, so maybe it's a factor.
this may have the good result of reducing total domain names selling the same product, and also the not so good result of a single source dominating the serps.
how are blogs doing overall? I just signed up for a blah.blogger blog but haven't put up much of anything yet.