Suggestions for a batch audio converter?
FFMPEG and a simple bash script will get the job done.  FFMPEG is the same set of libraries that are included with products like Handbrake.

The basic syntax is very simple:

ffmpeg -i inputfile outputfile


If you wanted to convert a FLAC to MP4, you would simply enter

ffmpeg -i inputfile.FLAC to outputfile.MP4


To convert a number of files a simple bash script like the one below will convert 

for file in /foo/bar/*.mp3
do
    fullfilename=$(basename "${file}")
    filename="${fullfilename%.*}"
    ffmpeg -i "$file" "/foo/bar/converted/$filename.mp4"
done


This basic script parses through a directory, takes the original filename, then removes the extension so a new extension can be added during output.