Hi Frank,
now that is interesting. Thanks for your testing.
I set up a share on a Windows 10 PC and played the test file (Pi 3 + DAC+, over wifi) multiple times. Every time the channel swap problem occured, although sometimes it took some minutes of playback.
If you want to do further testing without being bothered by the sine tone, you could just play the file on repeat while the balance knob is turned all the way to the left. If a beep appeares, that is a channel swap. If not, last thing I could imagine is that my Pi is defective.
Tobi