With the plugin enabled in my 3.2.1 multisite network - whether network activated, or only on the primary blog, the network admin menu loses its settings and theme menus. Deactivating the plugin restores the menus to the network admin menu.
I haven't the time at the moment to install a stock multisite setup with no other plugins installed to determine if it's due to a conflict with another of my installed plugins, so can't rule it out.
Have you run into this before?
