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.
HD-DVD: 55 / Blu-ray: 97
newest: Brotherhood of the Wolf / Kingsmen, How to Train your Dragon
AVR: Marantz SR6006
F/C/R: Polk RTi A9's / CSi A6 / Speakercraft AIMWIDE 3 / Sub: SVS PB12-NSD
SonyXBR-75X940D Samsung BD-P2550, Toshiba HD-A30, Nvidia Shield TV (2015), Xbox360 Elite, PS3, WDTV Live