Jose, the two sets of crossover settings aren't actually greatly different, i.e., about 20Hz. The Audyssey measurements indicated that those frequencies were the point where those speakers were 3dB down. For the M60s it was below the lowest 40Hz setting, so instead of a crossover frequency, the M60s were sent the full range, including the lowest bass.

The fact that the speakers were capable of handling those frequencies doesn't necessarily mean that that's the best overall result, especially when you have good subs like the STF-2s. My suggestion would be to take some of the lowest bass load off the M60s and put it on the STF-2s which are designed to handle it best. In short, manually set an 80Hz crossover for the M60s, raise the VP150 to 80Hz and keep the QS8s at 80Hz.
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Enjoy the music, not the equipment.