I noticed today that the front site of my multisite installation was presenting the content of of of the blogs (subfolder). Clearing the cache resolved the problem, for a while.
I checked the .htaccess file, and i saw that it contained the /subblog folder name of the blog that was presented!
I can only imagine that this was due to that i had been editing that particular blog, then entered the WP Cuper Cache settings and pressed the update .htaccess button.
It would be nice to see this resolved so I don't make the same mistake again :-)