Conversion to .m4a silently fails 100% of the time.
Running the convert-2m4a.sh script manually reveals this error message in conversion.log:
output file exists, use --overwrite option
Apparently gtkpod's conversion script is running faac on an already-existing output file, which causes faac to fail since version 1.29.5, when the --overwrite option was introduced.
Adding --overwrite to ENCODER_OPTS fixes the problem. (This might break compatibility with faac versions more than three years old.) Patch attached.