After multi-site setup comments and links don't work

This is in the root directory of my 706backup.com directory. All the other sites are subdomain sites under this one.

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RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ - [L]

# uploaded files
RewriteRule ^([_0-9a-zA-Z-]+/)?files/(.+) wp-includes/ms-files.php?file=$2 [L]

# add a trailing slash to /wp-admin
RewriteRule ^([_0-9a-zA-Z-]+/)?wp-admin$ $1wp-admin/ [R=301,L]

RewriteCond %{REQUEST_FILENAME} -f [OR]
RewriteCond %{REQUEST_FILENAME} -d
RewriteRule ^ - [L]
RewriteRule  ^[_0-9a-zA-Z-]+/(wp-(content|admin|includes).*) $1 [L]
RewriteRule  ^[_0-9a-zA-Z-]+/(.*\.php)$ $1 [L]
RewriteRule . index.php [L]

Ok, I updated my htaccess file with what you suggested and dropped it into the root directory. No change. What else should I do?

Yes, I can get into the admin area of each site. I am the sole user/admin and am able to do anything and everything in the dashboard for each site. I don’t know what you mean by resaving permalinks. How do I do this?

Ok,

I think i fixed it. I changed the permalink setting just for the test.706backup.com site and all the links seem to be working. I changed the link structure to http://test.706backup.com/index.php/2011/06/13/sample-post/

If I update all of the sites with this permalink structure do you think there will be any problems this might create with multi-site? Thanks alot for your help on this!