The default .htaccess RewriteRule to redirect every multisite.com to www.multisite.com does not work properly.

If you have problems with it, leave the two lines uncommented, and add the following three lines for each multisite you set up:

 RewriteCond %{HTTP_HOST} mysite\.com$ [NC]
 RewriteCond %{HTTP_HOST} !^www\.mysite\.com$ [NC]
 RewriteRule ^(.*)$ http://www.mysite.com/$1 [L,R=301]

Credit to Florian.