I am not familiar with your type of setup, however, I will say that I believe that .wav files are natively compatible with iTunes. Are you running 16 or 24 bit files? What is your sample rate? Where ever your problem lies, I don't think it's with iTunes.
Apple Airport Express won't play WAV files
My music is all on my iMac HDD. It is connected over wireless network to an Airport Express, which is plugged into a Marantz SR7007 using an ethernet cable. When I attempt to play a WAV file, I get a message that says "File Format Error". How do I play WAV files on this system ?? Thanks