I was able to recently get my wordpress multisite working for all subdomain sites. It works great now and clears the cache for an individual subdomain site on the network. Here is the thread about that change.
Now I have run into another problem. It appears that the super cache plugin is not clearing the cache when new pages or posts are updated for domain mapped sites. I have the domain mapping plugin box checked in options. I am wondering if this is related to the wordpress MU upgrade to multisite again.
I did a test on a new multisite network (not upgraded from MU) and the domain mapping tool is working as expected... but it is not working in my network I upgraded.
I am wondering if you can tell me what the plugin is looking for in order to do the domain mapping bit. Is it something in the wp-config file like the multisite one was doing? I have the "define('WP_ALLOW_MULTISITE', true);" in the config file now, but not the "define( 'MULTISITE', true );" because calls a different database structure.
Thanks for any help you can offer.