I too would bet on your speakers and room acoustics...however the audyssey processing in that unit should provide excellent correction, assuming you're using it and set it up correctly.
Keep in mind that the 5:1 audio sent with HDTV signals is not always wonderful (to say the least). Often the stereo signal is actually better.
Have you tried reversing the polarity on your center channel speaker? Sometimes this makes a big difference.
I doubt that replacing the processor will fix your perceived problem.