Check under Settings > Music Settings > Output Frequency. Make sure it is set to 44.1/88.2/176.4 kHz, and not 48 kHz (the default, I believe). The non-integer upsampling to 48 kHz, does indeed sound poor, but the 1x, 2x, or 4x upsampling sounds as good as any other player.

Pioneer PDP-5020FD, Marantz SR6011
Axiom M5HP, VP160HP, QS8
Sony PS4, surround backs
-Chris