Audio line-in port stopped working properly

I started to have a perplexing problem that I narrowed down to the audio in-put port on my Mac Pro (MacPro3,1). It was working fine then the sound level increased and the quality became distorted (like a "fuzz base" but affecting all sounds).
I was in the process of digitizing records, and believed the record played broke. So I got a new record player (audio-technica AT-LP120-USB). The same thing occurred with the audio in-put port, so I switched to the USB port and the audio was fine. I also checked with music already on my HD and it played fine. Consequently it has to be the in-put line port and/or a software issue.
I checked BBs but could not find a similar issue.
Any suggestion? Thanks in advance.

Since this is a Mac Pro question I'll request this be moved to the Mac Pro forum. You posted in the PowerMac forum which is pre-Intel Macs.

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