Preamp makers make their preamps out of phase (going out the amp outputs) usually because less is more. Their designs are simple and clean (and out of phase), and would require an additional gain stage to bring them back in phase. The addition of another gain stage would degrade the signal.
Conrad Johnson preamps are out of phase. You could call them or drop by on your way around the beltway and have them explain it better than I can. They are behind the Home Depot at Route 50 and Route 29 in Fairfax.
Sometimes CDs are recorded with the polarity reversed (by mistake), but reversing wires won't help. It needs to be corrected at the DAC. Some CD players have a switch on the remote to reverse the polarity for these CDs.