I remember hearing that when Pacific Assault was first launched, they were indeed using the Q3 engine at the core but it was altered so radically that it was almost unrecognizable.It's not only unrecognizable there is even nothing left of the Quake III engine. It's now pure D3D.
To make this "what engine" discussion end once and for all:
http://www.mohadmin.com/2004light/index.php?id=91