Greetings!
I have the same problem, using Sonic Foundry's Siren to perform the encode. Joe D'Andrea dug up / showed me an article where it might be a problem in the underlying encoder engine, shared by many ripper applications.
Roger promised a fix in the next release (see
this thread) for wiping the metadata.
I hope the metadata wipe is enough to fix it. I shudder at the thought of having to reload the empeg... With my latest audiobook purchases, I will probably fill the hard drives to capacity (Dirk Gently's & Harry Potter books). Now if only IBM and Toshiba will come out with those larger drives...