Domain Mapping subdirectories – them not showing up

I have set up a wp multi site opted for sub/directories
I have mapped the second site

I am able to put in mydomain.com/site2 and it resolves to the
mapped domain so that is all working

Problem is when you enter mydomain.com/site2 or the mapped domain url the server returns the file directory not the wp theme (wp theme is visable for edit / dashboard on the network) IE cgi bin of the mapped domain

I have the mapped primary domain listed as a add on domain in cpanel
there is an a record pointing to the server address which is a shared hosted isp.

everything works but the mapped domain is not pointing to the wp virtual theme that has been mapped.

I am sure it is something in dns or domain set up any ideas

Thanks
Rich