I soloed the track, bypassed the master effects, and exported to both wav and mp3. Turns out, the WAV sounds fine but the MP3 sounds choppy. So there must be something inherent in the track's recording that doesn't lend itself to MP3-ization. Does anyone know what that might be?
No, you have not determined that the problem is with conversion to MP3. That would be an extremely unlikely phenomenon. You have not determined that there is not some problem with routing from Sonar into Sonar's MP3 converter i. e you have not eliminated problems within Sonar. In order to do that, you need to do as you were previously advised. Take the wave that you have (which sounds fine) and use another program to convert it to MP3. That will eliminate Sonar from the test. If that MP3 sounds fine, there is nothing wrong with the mix per se that makes it problematic with MP3 conversion. Then re-import a good wave into Sonar, and export it as an MP3. If that MP3 is good then you can assume there is nothing wrong with the Sonar MP3 encoder.
It is conceivable that there is something unique about the frequency of the effect that is captured on MP3 conversion, at a specific bit rate. It could be that the high point of an echo for example is caught on sucessive samples in the MP3 conversion effectively "strobing" the effect. But daveny5 has suggested a test for that. If the MP3 only sounds choppy at one conversion rate, but not at a higher conversion rate, that would be highly suggestive that you have a problem with the wave itself.