Hi Steve!
With the latest beta and an album (FLAC file with embedded cue) in the "Now Playing" window, if i send the tracks as always do to my device (Sony Walkman), after encoding (AAC), artist and album folders are created correctly as always but inside the result is one file only with the same filename of the FLAC file and even the FLAC extension, instead of the correct M4A tracks. I reverted back to the previous beta for now.