I recently got a new A/V reveiver, with digital audio inputs.  Prior to that I 
had been using the analog outputs of my Squeezebox.  When I got the new 
receiver, I attached the SB to it using a TOSlink cable.  Shortly after moving 
to the digital audio connection, I played a song with very clearly 
differentiated left and right channels, and I noticed they were reversed.  I 
verified that speaker cabling wasn't the problem.  Then I attached a CD player 
to my receiver using an analog connection, and I played the same song.  The 
channels played correctly.  I then unplugged the power from my SB, removed the 
optical cable, reseated the optical cable, and restored the power.  This time 
when I played the song, it played correctly.
 
So for some reason, the channels were reversed, but they were restored after I 
power cycled and reseated the optical cable.  I haven't yet tried power-cycling 
again to see if I can get them to flip-flop back to the incorrect state.
 
I remember someone reporting a problem similar to this early in 2004, but then 
I never heard about it again.
 
I'm running server version 5.4.0 on Windows XP, and my firmware level is 40.  I 
do have the graphical display.