I record my shows with sagetv. I have been running this command below and the files that come out look real good. Most of what I have tried it on was already wide screen H264 files so I may need to revisit some of the details when I find some 4:3 shows but this command line should work for guy having sound issues. I also had the sound problem for a while. At first I was just converting to acc and getting no sound. I think my files were originally recorded in acc but 5.1 channel. It appears that was causing the droid to barf as I was getting no sound when using 5.1 but when I went to -ac 2 (2 channel) I started to get sound.
-t 60 is just to create 60 seconds for testing purposes. You can google ffmpeg binary to find the exe version and to get a list off all the command line switches
This may not be the best answer but this is a working answer for me.
C:\ffmpeg\bin\ffmpeg.exe -y -i v:\shows\med.ts -t 60 -f mp4 -s
848x480 -acodec libfaac -ab 128k -ac 2 -vcodec libx264 -qscale 10
v:\Transcode\test4.mp4
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