My disc comes with a 96kHz DTS stream, but the extracted result shows as 48kHz. Why?

This is a known limit. For DTS-ES and DTS-HD MA streams which come with a core stream and one or more extended streams, only the core stream (48kHz) is currently decoded by DVD Audio Extractor. And this limit only exists on DTS format. For all other formats like MLP, TrueHD, LPCM, etc, all sample rates are supported. We do look forward to adding full DTS support in the future.