My AC3 encodes play perfectly both native and streaming. I use the 3.11 codec and Gordian Knot (not the Auto version since it uses a newer codec). I assume you've tried the movies on the PC and they do play with audio right? No one else has ever reported this issue so I would troubleshoot by:
1) FTP the movie to the Xbox - does it play from the harddrive? (can't be a network/streaming issue)
2) Try a movie and encode with a different encoder (or just strip the sound out and remux using a different encoder. (this should narrow down a software issue for you)
The only anomaly I find with AC3 is that the soundtrack tend to be of lower volume unless I adjust for it. If you can provide the software you are using along with the codec it might help.
Some thoughts to get you started but I'm betting it has something to do with the encoding process you are utilizing. If you want to use Gordian Knot and you aren't already familiar with it there is a tutorial link in my signature.