Re: Filter site_url() to always point to main blog/site (Help request)
For setting the user domain, bp calls following function
bp_core_get_user_domain() and It has a filter bp_core_get_user_domain, but I am little hesitant to change something with this, as It may affect the other behaviors. Please check that function and bp_core_setup_globals() for more.
As far as I think, please check again and make sure you have not enabled the Multiblog mode(sometimes we may do it for testing an forget,specially my own experience), the subdomains in the userdomain is mostly a result of enabling multiblog mode.
Hope that helps