How are the speakers set up for testing? Are you substituting them in/out of the exact same spot or do you have both sets on the floor at the same time? If both are set up at the same time then one set will invariably have placement advantage over the other. I would also try disabling the MCACC and just keep the channel level settings, unless you've already determined that you prefer MCACC on for both sets of speakers.
Your room / listening evironment can have an impact on how speakers sound, as can your ears (ie. personal taste). It's natural to like one over another, but if you really want to make sure you gave them both a fair shake then you need to try and make the playing field as even as possible.
