One possibility: when you split out using mplayer you are getting silences /
discontinuities in audio filled with silences so when you re-encode sync is
good.
Obviously, if mencoder doesn't do this things won't work so well in the
presence of discontinuities. Similar problems sometimes occur when
people try to re-encoded MPEG from DVD or DTV with silences / sequence splits.
Andrew
PS
I wouldn't give up on checking very carefully the differences in the setup.
If you can turn on the logging INFO: messages and carefully compare what
you're getting for the two types of re-encoding...
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