Actually, if he replayed the mp3's on the Amiga with some crap AHI-settings and/or bad mp3-decoder, then the IFF-file might actually sound better on the Amiga 
Also real time playback of mp3 on the Amiga was pretty CPU intensive, you could help it by dropping the quality. If that is what he is comparing then it may be true. Although the mono/stereo thing sounds like something in his Amiga may have been broken, once in IFF then stereo should be fine.
Having the AHI sample rate set low could explain his problem. Or if he was outputting 14bit audio and it was't calibrated properly.
I'm intrigued what setup he had, an 030@50mhz (which is what I had) was still too slow for full quality mp3 playback.
I quite like the crunchy sound of low sample rate audio after hearing digital samples on the c64 for so long, so it didn't bother me that much.
