Hello what I can see from the KUKA's market place when ordering the spare parts, that in the Sunrise cabinet the "CPU quad-core Skylake LGA1151" is used under the bundle content for the SUNRISE spare part and for the Compact cabinet spare parts bundle it is used "Dual Core CPU CPU dual-core Skylake LGA1151". RAM's are also identical in both cabinets.
When exchanging motherboard's did you used also the QUAD processor from the SUNRISE cabinet or did you leave the DUAL core proccesor from the Compact cabinet? maybe that has something to do with compatibility. Because trying to order a spare part from market place it gets you to the same page for motherboard with same article number, either going for the parts for SUNRISE or KRC4 Compact, so I think that would mean the same BIOS with same settings I guess, regardless the controller. Only difference is with processor which is mounted on the motherboard when ordering spare parts.