OK, the standard 3-pin XLR pinouts are pin 1 - ground, pin 2 - positive (hot), and pin 3 - negative (cold). However, American companies used to (probably still) use pin 3 "hot" and pin 2 "cold". On some devices, there is a phase inverter, for example on your PerfectWave DAC II (don't know the exact pinouts it uses).
In a speaker system, you just swap the +/- on speaker side or the amp side to correct the mismatch between the source and the amp. I guess it's a bit harder in a headphone system.
are you sure your CD player is pin 3 hot? pin 2 hot has been the standard of the AES for 20 years