The problem is that LAME 3.99.5 is automatically converting the data to a lower rate when the VBR quality is set very low, which means the rate and length of the sample no longer matches the original, and it sounds detuned when played at the original rate. That seems to have begun in LAME 3.98. I'll update the MO3 encoder calibration to check for that. In the meantime, it's probably best to stick with LAME 3.97 or older.