I wish I had an answer for you but I wanted to chime in that I'm having the a very similar problem and wanted to throw some more info at it. I had multiple virtual hosts running just fine under 9,04 + Apache 2 + PHP 5.
Going from 9.04 -> 9.10 I now have all of my src="/foo/bar" trying to pull from /usr/share/foo/bar instead of what I set docroot to in the virtual hosts. Pages themselves execute via PHP just fine, Apache just seems blind to the Virtual Host instructions.
No conf files and/or php.ini have changed.. I recursively chowned the docroot's group to what apache is running as (www-data) in case it was a permission issue. This is all running on localhost (my dev environment).
Any hints would be fantastic.
Example log entry of what used to work:
[error] [client 127.0.0.1] File does not exist: /usr/share/javascript/supermenu.js, referer:
http://www.url.com/
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