Mentioned in [22418] on Core SVN:
When using WP_User::set_role() to set the role, don't unset all caps when the requested role matches the current role.

Created ticket #18934 on Core Trac:
Multisite issue cleaning up empty capabilities

Created ticket #18932 on Core Trac:
WP_User::set_role

Created ticket #18931 on Core Trac:
WordPress Multisite generates site URLs with http in SSL mode