New Blog Template plugin not copying uploads directory

Obviously, the directory isn't called uploads if using 3.0 multi-site, but either way, the directory isn't copying on new blog creation. Is this normal? If not, does anyone have a suggestion on how to solve this issue?

For example: /wp-content/blogs.dir/4/files/2010/.. => /wp-content/blogs.dir/44/files/2010/..