There are two different things mentioned here.
First, wpmu will strip any leading www from the domain you want to create your blogs on. It will do this (imho kinda stupid thing) regardless whether you want you blogs organized by domain or by directory structure. I agree that this is a difficult topic, but stripping the www no matter what isn't a solution either.
Next thing to mention is that *IF* you want to use the directory structure, the FIRST blog you create (e.g. the one you create when installing wpmu) has to be named "blog". If you give it any other name, you'll end up with the mangled name structure ekusteve reported.
In addition, there's an error in the provided .htaccess file that will show when you're using the directory structure method.
RewriteEngine On
RewriteBase /aktuell/blog/
# Rewrite http://www.domain.com to domain.com
RewriteCond %{HTTP_HOST} ^www\.(.*)
RewriteRule ^(.*) http://%1/$1 [R,L]
Actually, this will not only (again and quite unneccessarily when using directories) strip the "www" part from the domain. It will also (for the RewriteBase ist set to some other directory than /) strip the given path as well.
So either comment out the two last lines of the snippet above if you're using directories (and make sure you've got a "ServerAlias yourdomain.tld" - without the www in your Apache config) or add the missing path from the RewriteBase statement so that the two lines will look like this.
RewriteCond %{HTTP_HOST} ^www\.(.*)
RewriteRule ^(.*) http://%1/pathto/blog/$1 [R,L]
Took me some hours to figure that out.
Oh, should work for 1.0 and the nightly from yesterday.