@TK.
Wow, it's been almost a year since I followed up on this..
I still have the problem. All my cores have the latest firmware installed, and have correct device id's and respond when I query them with MIOS.
Just the cloning wont work, and selecting SID 2..4 from the control surface says "CAN DISABLED".
I have almost exactly the same pcb next to it, stuffed with same parts, which does not have the issue. Checked D1_COREx orientation, R80 and such. Removed all cores, checked continuity between D1_COREx's and their respective pin on the CORE
Quite clueless atm. Hints are welcome :)