Thanks all for the replies and your help.
Jim- I see no differences between the tags in PMW and the tracks viewed in explorer.
Shieber- I deleted the mpl files and had the player recreate them. The songs that are not visible on the Pono are listed in the database file.
Frobozz- You are right; the only files missing from the Pono are tagged <Field Name="Channels">6</Field>. As an experiment, I copied songs from 17 albums that are 5.1 or quadraphonic and the Pono recognized none of them

I have two-channel mixes of most of the albums and understand I can downmix in PMW/MC but it's a shame these aren't natively supported. Does anyone know if that's a hardware limitation or something that can be fixed/upgraded via firmware?
Anyway, problem solved (ish). Thanks again all.
-B