Is it possible to setup a domain mapping network if the main network itself is on a subdomain ?

I understand that the main site of a network using the Domain Mapping Plugin can not use a www prefix ( http://www.domain.com) url and should be run as just domain.com, however I have a multisite network which i'm trying to setup where the main site of the network itself needs to be a sub domain ..

Here's my setup;
* the network will reside at network.mydomain.com (because mydomain.com is already in use)
* I'm using a subfolder rather than subdomain option for the network setup.
* sunrise file is in the correct place and is tagged in the wp-config file.

Here's my problem ;-(
* I've setup a new site on the network which I get to ok by going to subdomain.mydomain.com/newdomainsite
* I want to point http://www.newdomain.com to this network site
* I've added the A record for newdomain.com to point to the IP address of the network
* I've setup a CNAME of http://www.newdomain.com to point to newdomain.com via dns
* If I browse to either http://www.newdomain.com or newdomain.com I just get sent to the homepage of my networks main site ... which is subdomain.mydomain.com/

The site is on a dedicated server (on amazon ec2) and has a dedicated ip address. The new domain arrives at the network but doesn't get mapped to the sites subfolder ?

Any help would be appreciated thanks