The noise your talking about is normal, my twin 350v3's do the same thing the first time they receive a signal. I think it will do this no matter if you have the auto-on feature enabled or not.

If your subs are up near your mains, you should use 0 phase, in fact, in most situations it is recommended to use 0 phase even if subs are placed around the room, I would not really on bass tests.

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