<font face="Verdana, Arial, Helvetica, sans-serif" size="2">Originally posted by xyzzy:
I believe this has changed and you now earn miles on all Virgin operated flights, system wide. You only earn EQM on transatlantic flights, though.</font>
xyzzy is absolutely correct. As of August 1, it does not matter whether you are booked on the CO flight number or the equivalent VS flight number if it's a transatlantic flight; i.e. you will earn EQM's on VS metal no matter how you are ticketed.
This was reported about a month ago:
http://www.flyertalk.com/forum/Forum20/HTML/008883.html
Cheers,
Brooklynflyer