To my knowledge, there are no overriding files in EAW because I've been dealing mostly with FOC. I haven't dealt with EAW mods in a while. All I have there is the stargate mod. I might have installed the "official" RAM fix, but would that be affecting this?
Also, was the installer supposed to only install Art, Audio, and Text files in \mods\Phoenix_Rising_v1.2\Data? All the other mods I have, including PR 1.1 have at least XML and Script folders...I know I have a full download because I checked the data size on Moddb with what I downloaded. I'll try downloading it again, but I don't think it will work...