Did you check the properties of the actual files to make sure that they were actually ripped at 48khz? I say this because my pc's soundcard was set to output all audio at 48khz when i first got it. I had to manually change the setting to allow it to send audio in its original form.
Worth a look before you go through the hassle of ripping that stuff all over again.
AVR: Denon X3300
F/C/R: Polk RTi A9's / CSi A6 / Speakercraft AIMWIDE 3 / Sub: SVS PB12-NSD
Sony XBR-75X940D, Toshiba HD-A30, Nvidia Shield TV (2015), Xbox One S, PS3
PC: Core i7, 16GB RAM, 512GB ssd + 4TB hdd, GTX 970 SSC