Just did a fresh install of WordPress 3.2 for testing purposes. After installing Multi-site via http://codex.wordpress.org/Create_A_Network the permalinks for posts and pages are broken. This is a repeatable behavior.
Below is an example from my test site and I've just changed the domain to site.com as an example:
With the default install of 3.2, this permalink will work just fine. Apache throws a "Not Found" error after installing Multi-site.
NOTE: The permalink for the default post in my default install of 3.2 is: