Gentleman, I may have had a breakthrough ( a knowledge breakthrough, not success with my issue here). I came across a thread here: http://www.gearslutz.com/board/high-end/686989-distorted-guitar-resonance-whistle.html (really just look at post #9 in there) that talks about a similar issue, mainly the DAW's (Logic in my case) reinterpretation of distortion. This issue is with distorted guitars (I hardly ever seem to record clean or slightly overdriven, but rather pretty high gain guitars) and so I wonder if this is the case with my problem.
Again, though, I'm not using the computer's soundcard, the POD is going into an Apogee Duet which as I understand it, takes the place/bypasses the soundcard.
Another reason I think it might be something in the system (i.e. not the POD's fault) is because, and I forgot I did this which is why I didn't bring it up earlier--I took the emulator output from my Blackstar HT-1 amp (this allows you to not use the cab/speaker and run a cable right out of the amp head to your recording device) just to see how it sounded. Again, sounded Ok in the monitors when simply in record mode with input monitoring on, sounds worse/different/muffled AFTER recording was made listening through the exact same gear.
So. . .system issue then? Is this a thing anyone's ever come across?