I have an Onkyo NR 3007 and currently a 4.0 speaker setup. I did run several audyssey setups but I do always get a scratching noise on my right front channel. I can attenuate the noise by setting the audyssey reference level to 15db, but this will not eliminate the noise completely. Onkyo support could not discover anything unusal with my device. I get this noise whenever audyssey processing is engaged.
Now the funny thing: As soon as I enable the subwoofer in my speaker settings the noise is gone! I don't hava any sub attached. I don't know what influence this will have on audyssey processing but did someone observe some similar effect?
I'm not Chris, but if I had to guess, you have a blown woofer in your speaker that is only becoming obvious when there's more bass sent to the speaker (which could also be why enabling the subwoofer makes it stop). What you're describing sounds like what happens when the voice coil gets knocked out of whack and grinds slightly against the magnet or former. You can verify this by swapping your left and right speaker and seeing if the crackling moves with the speaker. If it does, odds are good you have a blown driver. If it's still in the right channel, then the problem is in your AVR.