If the transpose led on the front panel is set to 0 that doesn't mean the GLOBAL transpose is. It can be as high as +-6 semitones before the LED changes position.
Config -> Global Tuning -> Master tuning = 0, Pure Tuning = Tempered.
If this is already right, try to see if there's any inconsistency between converters' frequencies (changing the converters' rate changes the recorded pitch)
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