I'm using DVD Audio Extractor to extract the audio from some Genesis re-releases that include DVDs (not DVD-A, but DVD video) and the packaging and graphics claim the 5.1 DTS audio is in 24bit/96 kHz audio.. the problem is that DVD Audio Extractor shows that both the Dolby Digital and the DTS are sampled at 48 kHz rather than 96 kHz.

Does anyone know how I can tell for sure which it is?

DTS96/24 is an extension on (standard) DTS. Decoders that cannot handle this extension decode just the "core" DTS part which will be 48kHz into 24 bits.