I've just been attempting to upgrade various sites that I have installed on the same codebase to Drupal 7.
I've run update.php on a couple of the sites & everything appeared to go smoothly. It dropped me back to the admin page afterwards.
However... I found straight away, that any admin pages that I clicked on gave a "not found" error.
Looking into it in more detail, I noticed that the admin page it sent me to was at http://mysite/?q=admin but the pages that are not loading are all using the clean urls. I can go to the page to test clean urls, if I type in the non-clean url address for it, but it shows up a 404 after I hit the test button.
At the moment, I can't manage to do anything much, as Drupal seems to think clean URLs are working, but clearly they are not.
Clean URLs worked fine with D6.
I've checked that the .htaccess file uploaded correctly. I had never customised the .htaccess file with D6.
One factor that may be relevant is that I run drupal in a sub-directory, but with the re-write configured not to show the sub-directory in the URL. I've had it set up this way for years with no problems & it doesn't involve the .htaccess files within the Drupal directory.
Setup is as follows:
/cms (this directory is the base drupal directoryl)
/site1
/site2
etc