iPod don't naively handle FLAC and converting to ALAC from FLAC is normally a two step process. FLAC -> WAVE -> ALAC. iTunes don't understand FLAC and as far as I know now other tools write ALAC, this will change that.
"The eleventh commandment was `Thou Shalt Compute' or `Thou Shalt Not Compute' -- I forget which." -- Epigrams in Programming, ACM SIGPLAN Sept. 1982