It is very common for the automatic setup to mistakenly call a "small" speaker a "large" one, but not so common for it to make the opposite mistake. My guess off the top of my head is that there may be a dip in the frequency response, possibly due to room placement, at just under 160 Hz for your main speakers.
What I recommend, after you make sure you have everything where you want it, is to "correct" the errors in the manual setup after having run the automatic setup (making sure the microphone is positioned in accordance with the manual's instructions). When I do the auto setup with mine, it "decides" that all my speakers are large, sets the crossover at 40 Hz, and sends the bass to both the front and the subwoofer. I change this to have every speaker set to small, move the crossover up to 60 Hz (and am thinking about setting it at 80 Hz), and send the bass only to the subwoofer. It does, however, seem to get the delay (distance) right and the level seems good, so I am glad to have the automatic setup.
Just to be clear, you have the CM7, CM1, and CM Centre, right? Oddly, according to B&W's web site, the front CM7 speakers have the -3dB point at a higher frequency for the bass than the smaller CM1! In your case, I would set the crossover at 80 Hz, and make sure that all the speakers are set to small. If B&W's web site is right, there is something odd that they are doing with those front speakers.
And one more thing: A speaker whose -3 dB point is at 62 Hz is not what should be called "full range", so your front speakers are properly "small" in the receiver settings. It is not a question of how big the speakers are physically, it is a question of how low they go before the sound starts to trail off that determines whether a speaker is "large" or "small" in the settings.