[spidergawd]

ffmpeg is cross platform, and seems to preserve tags.

ffmpeg -i inputfile.flac -acodec alac outputfile.m4a

I don't use mac or windows, so I'm not sure of the proper way to do it on those platforms, but to do an entire folder in 'nix I'd do:

for tune in *.flac;do ffmpeg -i "$tune" -acodec alac "$(basename $tune flac)"m4a;done