I have WP 3.1.3 set up as a multisite installation using sub-directories (rather than sub-domains). When viewing the SlimStat dashboard on any of my sites, say, blogs.myuniversity.edu/science, all hyperlinks (e.g. the Dashboard, Visitors, Traffic Sources, etc. tabs at the top; the Daily pageviews graph points; the 'More' links in the Recent Known Visitors widget; all links in the Spy View widget, and so on) point to blogs.myuniversity.edu/wp-admin/index.php
As such, when I click on any of these links my browser moves from my /science site to my / site - this is unfortunate, since stats for a particular site cannot be viewed without manual address bar manipulation.
A quick look at the code (e.g. wp-slimstat/view/index.php) shows that it is using
$_SERVER['PHP_SELF'] to create the link addresses. Changing all instances of this to
admin_url() or (more precisely)
admin_url('index.php') seems to rectify the issue for me.