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If you're really bothered by this, you can take solace in the fact that Google's new infrastructure, Big Daddy, has the ability to cache data from one bot's visit for re-use by another bot. In other words, if the Mediapartner bot visits first, it saves the page info in a cache at Google's data center, and Googlebot checks that cache to see if it can avoid recrawling the page. Result: You save bandwidth, and so does Google. Matt Cutts of Google describes this process in his "Gadgets, Google and SEO" blog.
On the other hand, the media partners bot no doubt refines the process and makes it more efficient as well as producing a separate index for AdSense staff to play with as they will...
AS can sometimes make a good initial guess for ads for a completely new page on its first impression from the following factors as far as I can tell:
1) The site content that G already knows about, especially pages close in the /dir/ectory/hier/archy to your new page.
2) Keywords in the URL (and any query parameters).
especially pages close in the /dir/ectory/hier/archy
Rule of thumb: Any speculation about how directory hierarchies influence any aspect of Google's activities whatsoever are dead wrong. They are invariably a result of making link structures that mirror directory hierarchies and then believing that it was the directory structure rather than the link structure that caused the effect.
[I report on my own experiments and ads and site, which is why I hypothesise this, but of course (a) YMMV and (b) I may well be wrong.]
In particular I notice that one component of my URI path often brings up inappropriate ads, where nothing else should. I don't see why G *shouldn't* parse the URI for *clues* for a new page and when it is otherwise struggling! I have discussed this with G and they do not reject my hypothesis...
And in the most recent instance which actually startled me with how accurate the ads were, the file name itself is the keyword, and the title text is also KW heavy.
If this improves targeting it indicates that the file name is very important because there was not a moment's hesitation, the page loaded with perfect ads as fast as my broadband loads any page.
For the record ALL my pages are in the root directory, only includes, images, scripts, etc go into sub dirs.
This is exactly how I have my sites setup Andrea99 and I have never had problems with off-subject ads.
In fact, the only links I add to my filter, are blatant MFA's and (believe it or not) two competitors.
I will not claim that this directory hierarchy is the sole reason for good ad targeting, but I'm sure it doesn't hurt.