Just to take this further:
This might be a problem, but from where I stand the only things that might contribute to that problem with tools like Google Analytics is:
1. That the code is placed before any real text happens (just under the <body> and by that taking valuable text space.
3. Even if placed just over the </body> this might also pose a problem, though less likely
4. Again the code itself or communications with the JS file might also pose a problem, though very unlikely.
It’s all about access, is it not?
Another scenario is that the cookie or the “harassment” that the search engine spider get’s hit by the analytics tool when visiting a site might be a violation to some “spam” detection and therefore flagging the site for some kind of penalisation and on this case lowering the the Page Rank.
Google is a huge company and the left hand might not know what the right hand is doing?
And to take it even further:
This is actually a discussions I have had in the past, generally with analytics code full stop, regardless of vendor are that they SHOULDN’T be put at the beginning of the page as this MIGHT (stress might) have an effect on page rank / visability.
I advise all of our clients to ensure that the code is in the BODY, just before the close tag. This is most SEO freindly.
The beginning of the page code is the most important in terms of page ranking and indexing etc.
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