I am using the latest versions of both WordPress and Buddypress and have installed multisite.
After installing Buddypress (and network activating it), the Buddypress admin showed up on the sub-sites (installed in sub-directories) as well prompting me to configure the component settings for each sub-site.
I know the admin should only show up in the network panel, not even the main blog admin panel, since it is network activated.
I've been struggling for a while and even created the bp-custom.php file, to no avail.
I have posted this issue on both Wordpress and Buddypress forums and was advised to post it here as it could possibly be a s2Member issue.