I have a favorite Polygon Window (a.k.a. Aphex Twin) cut, "Bike Pump Meets Bucket", which comes out gritty and clippy, and sounds truly horrid through headphones (about the only way I'll listen to MP3). Lots of my other electronic ambient came out sounding great with the same settings. This cut needs to be mellowed somehow. I'd welcome suggestions.

Encode again with a 15kHz lowpass filter. =)

Seriously speaking, try to re-encode with a setting like sfb21 -8?

Rather than having the encoder encoding the high-freqs incorrectly so that less high-freq is present I'd custom-EQ the track first using, say, Naoki's EQ plugin with Winamp before encoding.