I asked my colleague who designed the MADI card about this, and he said:
It sounds like a frame-mode issue, like gavvyt suggested on the forum. When operating at 96khz, we only support the newer 96Khz framing, not the legacy 48khz framing, which interleaves the samples. The 112D allows the user to select either 48khz framing or 96khz framing. So my guess is that he has the 112D set to [sample-rate=96khz, framing=48khz]. It needs to be set to [sample-rate=96khz, framing=96khz].
