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I don't think it can be anything like that. At first I thought it would be the missing
fundamental effect. If you would actually record low synth notes with a mic that can't
pick up the actual fundamental, or play it back through speakers that can't.. the ear
can still perceive the right tone because of it's higher harmonics.

Anyway, give us an update if you can Agent.

AxeD wrote:In Logic, middle C is c3 instead of c4. Does that have anything to do with it
by any chance? I'm just spitballing here, I'm not that familiar with the software myself.

It might have, but then it also means that all keys on piano roll are labeled wrong, because you can find the key that says "C1", but when you play it, it's C2. I don't think there's anything wrong with harmonics (like fundamental being quieter than normally, it's just that everything needs to be played 1 octave lower than usual.