I have things set up as follows.
Music library is all in Apple Lossless Format
The Pono is set up to sync a single playlist. The Sync options are set to convert to FLAC (so that the Pono will honor ReplayGain values).
First sync works fine, but after completing, shows that all the songs are "in queue". Sure enough syncing a second time converts to flac and copies the songs onto the Pono again so that there are now two copies.
Combination of this bug and the one where syncing doesn't delete songs no longer in the playlist makes syncing completely unusable for me. I have to manually delete all the songs from the Pono, then copy the playlist over again every time I change the playlist.