Regent - 4:38 pm on Jul 15, 2010 (gmt 0)
I feel your pain. The circumstance you are describing is a little different than mine and the sites I manage, but I believe the application is the same.
Over and over again, I have seen Google perform what I call "Google Background Check". In my cases, adding new pages or substantially changing existing page content triggers this check. In your case, it seems to have been triggered by code changes relating to site structure.
Nonetheless, the "Google Background Check" (at least in theory) says that if there is substantial change to a page, Google removes the page from rankings and puts the page into their "Background Check" process. This "Background Check" process could include many filters including:
PR contribution check
Keyword screening (for government)
These types of processes are extremely CPU intensive and could not possibly be performed in real time or on a regular basis. So Google MUST have off-line processing for these CPU intense processes.
It is logical that Google would perform this kind of "Background Check" when they see a new URL. But it is also logical that when an existing URL undergoes significant changes that a "Background Check" must be performed again.
It is this latter condition I am theorizing your site has been relegated. In most circumstances, I see new pages or pages with significant changes ranking within 4-6 weeks, but there are cases where I see it taking longer.
It seems that the more commercial a keyword (phrase) the more Google scrutinizes that page. It may be that Google takes a harder look at pages that are in more competitive spaces - just a guess. PR may also affect how Google prioritizes one page over another. Presumably, higher PR pages would receive a higher priority and go through the screening process quicker.
In any case, there is lots of empirical evidence to suggest that Google does perform some kind of "Background Check" process. The evidence suggests that is where your site is right now.
P.S. "You Can't Hurry GOOGLE Love" - a new tune sung by 'many webmasters' ;-)