No RM mixer here any more, so I can't check the issue, but what comes to my mind are the questions
a) phantom power switched off?
b) Zero Out scene loaded before switching to 96 kHz?
c) you are aware that the mixer has only half of its processing capacity @96 kHz?
I would not recommend using the 48/96 kHz switch like a normal on/off button. Do not toggle between the settings! Make the selection immediately after the mixer has booted, when the mixer is "fresh" and no known and unknown settings disturb. Recalling Zero Out scene often is important, because it makes the mixer work as intended.
If this does not help and you can't narrow the problem down further, open a ticket at PreSonus.
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