While most of my music is encoded as 44.1 kHz/16-bit FLAC from CDs, some of it is 88.2 kHz/24-bit high-res FLAC. I use the the on-the-fly conversion in MusicBee's device settings to encode all of my FLAC as ALAC (using nu774's refalac64) so the iPod can play it. This works great for all of the 44.1 kHz files, but the 88.2 kHz files remain at that high sampling rate (though it does reduce it to 16-bit). I've tried using refalac64's command line to do the downsampling, but that yields the following error message: "ERROR: floating point PCM is not supported for ALAC". Since MusicBee only offers to resample in the Format Converter dialog box and not in the device settings, I can't think of any other way to get it to resample the songs (when I do use the resample option in Format Converter, it does produce a good file). I've also contact nu774, but I haven't heard back yet.
I'm using: "refalac64 in.flac –r 44100 –o out.flac" in command prompt (slightly different for the MusicBee parameters)
Windows 8.1 Pro 64-bit