The strange thing is, I've tried using Foobar and Media Monkey with A) the original FLAC and AAC, B) an accurate/secure re-rip and an AAC made from it, and there is no problem. I then converted the FLAC to LAME and tried that on my S639, and there was also no problem. I even listened to the (pristine) CD itself, which was a bit nostalgic!
I guess this is probably a fault with the Sony rather than with Nero, but it's easier to get in touch with the Nero guys!
Sample in the uploads section:
http://www.hydrogenaudio.org/forums/index....showtopic=73275
(hopefully trimming the first 5 mins with dBpoweramp DMC hasn't messed it up.)