Hi there!
Tonight I've set hdmi_audio_96k=1 in my miSTer.ini. I use an HDMI audio extractor to convey digital audio in my Cambridge Audio DAC via Toslink cable. Cores like SNES or Amiga sounds WONDERFUL at 96khz (confirmed by the DAC display), but some cores (like C64, VIC20 and NeoGeo) doesn't emit any sound.
Maybe this setting is not supported by all cores?