What media player do you normally use for playing your FLAC files?
One strategy you could try is to convert a few albums to WMA-Losselss. Import those files in iTunes (iTunes for Windows will read in and then transcode WMA-Lossless). Then have iTunes transcode the WMA-Lossless to MP3 (or AAC) to put on the iPod Touch.
I haven't tried that configuration myself. But should work, and worth a quick experiment. WMA-Lossless is much more Windows friendly than trying to do ALAC on Windows.
I use J River Media Center and have J River convert my FLAC files to MP3 (Lame -V0) when syncing to my iPod Classic. I actually prefer putting high quality lossy on a portable rather than lossless. And trying to do ALAC on Windows is just too much of a PITA just for a stupid little iPod.