Have you tried using -af channels=nch[:nr:from1:to1:from2:to2:from3:to3:...] audio filters? Although, it's odd that the channels are only mixed up in Ubuntu. Have you tried using an updated version of ALSA?
** Changed in: Ubuntu
Assignee: (unassigned) => Matt Sicker
Status: Unconfirmed => Needs Info
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Incorrect 5.1 audio when playing DVD
https://launchpad.net/bugs/53516
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