Brian -
that came around with FLAC v1.1.3 (and continues with v1.1.4, as you've noted)
it's discussed a bit in this thread:
http://taperssection.com/index.php/topic,76692.0.htmlbasically, it's has to do with the two different file formats used for 24-bit audio. the "old" standard (the one that just about every program uses), and the newer "Microsoft" standard.
in CD Wave, if you check the "alternate format" box, you get the older standard. if you leave it unchecked, you get the "microsoft" standard
FLAC (starting with v1.1.3) will compress either file format, and will result in the exact same FLAC file.
if the 24 bit file is in the "microsoft" format to start, you won't see any warning message.
but if the 24 bit file is in the "old" format (much more common), you'll get that warning.
either WAV format that you use to start will result in the same FLAC file, and FLAC will decode to the files back to the "old" standard, no matter which WAV format was used to begin with.
I verified all this stuff with FLAC Fingerprints and wav md5's and stuff. it's all in that other thread that is linked to above.
am I rambling, or am I clear enough?