If surround speaker is crackly while attached to one channel but not to the other, I'd be inclined to believe your old Yamaha has a channel going bad. AFAIK there is no "sound like garbage" setting you have to disable.
Running YPAO couldn't hurt. Probably won't help, but I suppose it is possible that the speakers that were corrected previously had the bass boosted so much that it's playing through the tweet of your new speaker. A better indicator might be to turn YPAO off and test in pure direct.
Put it back on the wall and play it with the good channel again. Crackle still gone? Play left surround on the right surround channel, and right surround on the left channel. Crackle moved to the previously good sounding side? If so, your wiring is fine and your receiver needs to be replaced sooner rather than later.
Even though it's probably overkill for troubleshooting, make sure your source signal and your receiver are plugged into the same outlet to rule out a ground loop as the cause. I doubt it'll make a difference, given the troubleshooting you've already performed though.