uses avconv to convert .flac files to .alac. Is case-friendly and will skip files it has already converted. public domain where applicable. Come on, it's a 27 line bash script!

flac-to-alac.bash

#!/bin/bash

downloaddir=$1
if [[ -z "$downloaddir" ]]; then
  echo "fatal, no arguments given"
	exit 99
fi

find "$downloaddir" -iname '*.flac' | while read flac; do
	echo "found $flac"
	dirname=`dirname "$flac"`
	basename=`echo -n "$flac" | sed 's/\.flac$//i'`
	basename=`basename "${basename}"`
	fname="${dirname}/${basename}"
	if ! [[ -f "${fname}.m4a" ]]; then
		echo "alac "${fname}.m4a" doesn't exist, creating"
		avconv -i "$flac" -acodec alac -- "${fname}.part.m4a"
		if [[ "$?" -eq "0" ]]; then
			mv -- "${fname}.part.m4a" "${fname}.m4a"
			echo "success!"
		else
			echo "eek, something went awry: $?"
		fi
	else
		echo "file was already converted, skipping"
	fi
done

I use iDealshare VideoGo to batch convert FLAC to ALAC, it supports directly drag the FLAC forlder and then convert them at a time.

And it has both Mac version and Windows and also can convert FLAC to MP3, WAV, AIFF, AAC, WMA, and etc.

Step by step guide at http://www.idealshare.net/audio-converter/flac-to-apple-lossless.html