Sorry, Mac. I replied to your email before I saw this post. If that is the waveform display of the 3k before and afterwards, then of course, yes, you have a problem...

But, for it to pinpoint the 3k as the culprit, you need to make a recording of something else through your soundcard, to eliminate that as the cause.
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An arranger is just a tool. What matters is what you build with it..!