The csi5 has the capability of being turned upside down with the beveled edge down so it is facing more upwards. Will doing this help any?
I think that's your problem. Since the center is not delivering the signal directly to the mic, the mic is compensating by boosting the dB level of the center. Flip it over so it's angled to the listener. I own the CSi5. If properly eq'd, it will sound amazing.
Do you have bookshelves, or towers? Are the front mains set straight forward, or angled "in" just behind the listening position? Angling them in a tad will also affect how the auto setup calibrates the center channel's dB level.
One last item - once you're finished with the auto setup, don't be afraid to go in and tweak it to your liking. You can always cut the high end frequencies if your room acoustics don't do it for you.