Sustained notes played through iTunes waver in frequency-sounds sick

I up-loaded all my CDs to iTunes on my previous Mac (G4 iMac with the hemispherical base) and downloaded them to my 3 iPods. After that I upgraded to the G5 Intel Mac. Now, some songs with sustained notes played directly from the G4 waver in frequency sounding sickly. If I play or up-load one of the original CDs to the G5, it, too, sounds sick. These same songs on my 3 iPods still sound okay even though they’ve been synced to the new G5. I downloaded my library to the new iPod touch and the affected songs sound OK. What’s the problem? Have other people had this same problem?

Sure sounds like a problem with the audio circuit in the Mac Mini. 
The speakers you are using are they powered? Is there an amp involved in the setup? I'm not familiar with the particular model of Mac Mini, does the audio jack double as a TosLink connector (digital audio) as it does in later years models? If so and you external setup has the capability you could try going digital to see if that helps.
Finally if all else fails you could go with a USB to analog audio converter such as Amazon.com: Digital to Analog Audio Converter with USB ... for example (note I have no personal experience with that unit just throwing it out as one possibility).
Wish I had more for you
regards

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