Beta4Me:(this usually done on-the-fly by your ripping program in conjunction with an encoder).
C'mon, dont be nit-picky with me, the above is exactly what i meant
EDIT I'm not trying to be funny by the way, just to understand.
Let me clarify: You put WAVs into itunes, then "tag" them, before converting them to ALAC? Thing is, ALAC can, AFAIK, be properly tagged (none of that fake tagging where many things can lead to the loss of the "tag", which seems to be what you are describing). So, why not rip so you get on-the-fly ALAC compression (effectively, this is ripping to ALAC) and, therefore, a properly tag-able file?