I had trouble with multisites that was similar to what is described here. I found two issues with my configuration:
= If Apache httpd is using an Alias directive, then it should match the RewriteBase directive.
= I found two fields in the Edit Site screen named Template and Stylesheet. I believe that they should match the folder name that the theme files are located in. For example, the folder name for Twenty Ten is twentyten. Note that on my computer the folder names are case-sensitive.