When I play, I sometimes get extra noises out of my amp that has a "thuck" sound. I had heard it occurs from not keeping the pick perpendicular to the strings upon playing, but the sound was still present even when I tried readjusting the pick.

Is there any way to prevent this?
lower treble and mids. if you have an eq, mostly lower high mids. if thuck is what i think it is, it might be the high mids. or if it is the other thucking, you might have too much gain for your liking.
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Tell the little bitch behind your amp to stop kicking the speaker

edit: oh you've already solved the problem...
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