You're missunderatanding how it works.
It's SUPPOSED to point to /files/YYYY/MM/DD/Imagename.jpg -- We WANT that to happen. It's NOT broken.
Remember when I said this WAY in my first post?
WordPress smartly redirects the /files/ location to blogs.dir/#/files (where # is your site #).
Trust me. It's correct. It's working.
you point to http://name.domain.com/files/2011/05/image.jpg
WP translates that to http://name.domain.com/wp-includes/ms-files.php?file=2011/05/image.jpg (Remember? You tested that AND IT WORKED!!!)
And THAT gets finally parsed as http://domain.com/wp-content/uploads/2011/05/image.jpg
That whole process depends on a couple things, but most important is your .htaccess being able to do that middle step. YOURS fails. It is failing to parse this:
# uploaded files
RewriteRule ^files/(.+) wp-includes/ms-files.php?file=$1 [L]
That's why I had you test the URL with that format in there. And since THAT was successful, I know it's not WordPress breaking (because it can parse the image from that location), but your .htaccess, which means the .htaccess isn't handling redirects as well as it could. Which means it's the configuration of the server, which is handled in the httpd.conf file.
And at this point, I've given you the advice and directions I have. So you can either research it, google 'httpd.conf wordpress multisite', hire someone, or wait and see if someone better with httpd.conf rolls in.
(And posting in other peoples topics, when (1) you have your own and (2) You aren't having the EXACT same issue pisses people off and makes it MUCH harder to help anyone. Don't do it.)