It appears that changes to libav have broke alsa ac3 encoding. Below details a patch to fix the issue.
http://git.alsa-project.org/?p=alsa-plugins.git;a=blobdiff;f=a52/pcm_a52.c;h=76f21cd003bfcfb8c3b07e003f04aca6132a7b79;hp=ed491b31c32a87a65258524b497d05d6e876fc0b;hb=40c129a160f37fe9488b2828d6299f99c269703e;hpb=06ca71522f1dc48b8503d945da81fdbcbab0aafa
After implementing the patch and recompiling libasound_module_pcm_a52.so I have AC3 output once more
Update
A new libasound-plugins package is currently in oneiric proposed with the above patch included.
