Thanks for the responses. I actually figured out what to do. That alternate wave format is the trick, but i was using the save function in a way that the option was not made available.
I was tracking a flac encoded master. When I saved the tracks to disc, I expected a save without conversion would write out flacs. I wanted wav files so I selected "convert to wave". When the save dialog is in that mode, it does not offer the option of saving in the alternate format. So I got wav files that command line flac didn't like.
What I figured out is that if you are tracking a flac encoded master and you select save tracks with no format conversion, it actually does convert the format and save the tracks as wav files rather than as flac files. I think that dialog should include the "alternate wav format" switch when the format conversion is set to store as WAV and I think it should save the tracks as flac encoded files if the master is flac encoded.
In anycase, I know what I need to do to get the desired output.