I have exactly the same speaker set and tried many times to use the auto setup of the Onkyo 703. It never worked well.
I guess, the auto calibration is not sophisticated enough to take care of the room resonances. It senses a resonance, but it only has 5 EQ bands, tries to pull down one band, it distorts the other bands and so on. I always ended up with weird setting bouncing from +7db to -7db and terrible sound.
I ended up doing it all manually, set up the distance, equalize the speakers, and change the sub as it fits your taste. For me it's +4 dB. That's it. Takes a few minutes and sounds much better than anything auto.
