Please consider the broken link checker to work with wordpress-mu (mulitsites). I use wordpress mu and when I install broken link checker, it only works for the mainsite. When I run the plugin with my wordpress mu, it just checks the mainsite again.
Susan Morton commented
I activated this seperately on all sub-sites and it works on all sites but one, my biggest (most link-heavy) site. It just sits there stating no broken links and never updates.