using Audacity. > export files as raw 16bit PCM (as it opens them as 32bit).
In Audacity... Edit -> Preferences -> File Formats.... mine is set to "WAV (Microsoft 16bit PCM)" or "Other"/"Signed 24 bit PCM" if I'm saving to 24bit.
Then I flac from command line using "flac *.wav" with no special parameters.
"shntool len" is your friend... if it comes back with something clean like below you are good. By "clean" I mean all those hyphens under problems is a good thing. When you see "c" in the first column is means it's not 16/44100 CD quality.
>shntool len *.wav
length expanded size cdr WAVE problems fmt ratio filename
5:02.67 53430428 B --- -- ----- wav 1.0000 01_Track01.wav
4:13.46 44737436 B --- -- ----- wav 1.0000 02_Track02.wav
>shntool len *.flac
length expanded size cdr WAVE problems fmt ratio filename
2:35.41 27438476 B --- -- ---xx flac 0.4686 abb2008-08-16d1t01.flac
5:45.17 60898028 B --- -- ---xx flac 0.5861 abb2008-08-16d1t02.flac