I am using WP MU 3.5.1 and the latest development version of your plugin.
My primary MU site is installed in my server's root (domain.com). A secondary site (single installation without MU activated) is installed in a directory in my root as an add-on domain (domain2.com).
After installing your plugin in my primary's plugin-mu folder, when I goto the "Domain" settings I do not see the primary MU domain listed in there with ID #1. Is that normal?
I should also add that I cannot even add my primary domain as ID #1 because after I press Save, nothing changes.