To me, this doesn't sound like normal behavior for an encoder at all. Especially at 160kbps. This shouldn't happen at all, and even at very low bitrates this sort of thing shouldn't happen to a degree as extreme as you've described.

I think that you've got more problems, above and beyond the choice between Joint and True stereo encoding.

Perhaps there's something wrong with the codec, or maybe it's not set to "high quality" (some codecs have a speed-versus-quality choice you need to make).

And I still suspect that the problem might lie in the ripping stage rather than the encoding stage. Have you checked the raw wave file to make sure it's not hosed?

Also, have you tried other encoders/rippers?

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Tony Fabris