My pod XT pro has two different clipping notifications. Each go off at different times. There are two lights on the front, one for signal and another for clipping. And another Clip warning appears on the LCD at times as well. Which warning means what signal is clipping?

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Have you checked the manual?

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do you hear any clipping?

oh, and it might be because you have high-gain pickups. Digital stuff sometimes doesn't like that. If that is the case, maybe you want to lower the volume entering the pod's input a little bit.

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