Yes, the other controller blinks similarly it broke earlier.
I guess all the cubes are done. When I tried them with a working controller, the controller didn't boot correctly. I got light to only one led (out of 3) and blinking 'bright light'.
That's normally not good. The way to be sure is to test the cube with an ohm-meter/VOM for resistance. Check the resistance between pin 4 and ground and pin 6 and ground (on the 10 pin connector where pin 2 is the top left one and pin 10 is the top right one). If 0 ohms on pin 4 then things are complex. If 0 ohms on pin 6 the board is shot.
I'll buy ohm-meter and check, thanks! n00b question: what pin is ground?

e. I checked cubes and if ground is the pin 8, then 0 ohms between it and pin-4 / pin-6. So 0-ohms for 3 cubes, only one without 0-ohms was the one caused this mess (the one with bare atx-6 pins).
Pin 10 is ground, as is the three top pins of the PCIe plug.
And oddly enough that could make sense; when you shorted it the current flowed through all the other cubes, but since that one did *not* have a ground it suffered a different kind of damage. Sucks, I know but check again.