Same problem here - video (mpeg) SR's just fine but AC3 (5.1) sound does not copy (no recompression: stream copy). There are 3 AC3 audio streams (5.1 448 Kbps, 5.1 640 Kbps and 2 channel) MediaInfo shows ZERO channels after encoding. Interesting - when choosing the AC3 encoder option and hitting the configure button all options (bitrates and frequencies) show ZERO channels. So IMHO it has something to do with the source.
My video plays fine in all players using FFDshow video and audio decoders with AC3 spdif to my receiver. Tried WMAudio and got some sound but completely garbled - every 1 second of sound interspersed with 1 second of static.
Could it be the multiple audio streams?
Small clip:
http://rapidshare.com/files/352178758/Segment_0.mpg.html if anyone wants to give it whirl.