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Software will be identical, if you have the same firmware and the same settings (colorspace, saturation, contrast, exposure compensation, metering mode, custom white balance, and more). Are you processing the Raws in camera (direct to JPEG) or off camera (on a computer)? Is the processing identical?
If you have the same firmware version, then take both batteries out of all of the cameras (the rechargeable power battery and the small date-time battery) and leave them out overnight or for an hour or more. Turn the cameras on for a minute with both batteries out. Then turn them off and reinstall the batteries.
After resetting them like that, and with identical firmware versions, immediately take a pre-planned set of test shots without making settings. Compare those.