Wav to Ac3 works fine, but in the previous process you must do anything wrong.
Use eac3to or BeHappy to do the process directly without channel mapping problems.
For instance:
eac3to pal.ac3 -slowdown -448 ntsc.ac3
for 448 Kb/s, default bitrate is 640 Kb/s
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BeHappy, AviSynth audio transcoder.
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