Currently I'm having this issue: Firstly, let's say my main blog, the main WPMU install blog is running the default WordPress theme. Then I log into my second WPMU blog that I made, and change the theme over there to the Classic theme. The theme changed, as well as the main's! That is something that I find incorrect.
Also, I tried editing the "Hello World!" post on the main blog, and the same change appeared on the second blog.
Perhaps this is a bug? Do I need to reinstall my WordPress MU? Is there any changes I need to make in the settings?