Does the keyboard controller from the board that doesn't recognize the keyboard work on the other one? If so, that would discard the chip being blown.

Also, I assume you have checked for continuity across the fuse over the keyboard connector?

Yes, the keyboard itself is working.
I put a socket for the keyboard controller and tried few chips that work. The result was the same - no keyboard recognized.
The 4 fuses around the keyboard connector fine.

There are 4 (or 3?) inductors, but only one fuse (F1 or F2).

There are 3 of them. They appear fine.
F2 beeps the multimeter when measuring on both ends.

Maybe it has nothing to do, but I wonder what that voltage regulator below the keyboard chip does (LT1076)… after all that board is 5V only right?

It´s for the onboard CPU "IBM 486BL3" that needs 3.3V.

That voltage is actually slightly different for the BL3 CPU between the two boards. Which is strange.
(A while ago i asked another member here who owns Cougar board to provide the voltages he sees. He is about to come around on that.)

are you reading voltage coming from the keyboard connector?

Can you be more specific about the location, or simply where the pins connect to the PCB ?

Multimeter in the AT keyboard socket or the leads on the back of the AT keyboard socket. It is possible you have a broken AT keyboard connector or you have broken solder joint there. Cuz like if you plug in keyboard and you get no power than thats your problem. If it gets power but it doesn't input any characters thats a seperate problem. But both could be casued by a bad connector.

There is voltage on pins 2 and 4. That is on both boards.
The interesting part is that on one of the boards that voltage is 4.7V the other is 5.1V. These voltages are in line with what the VRMs output on the two boards.
That's why i asked that other member here to clarify what voltages he sees.

pshipkov wrote on 2023-01-17, 20:24:

The interesting part is that on one of the boards that voltage is 4.7V the other is 5.1V. These voltages are in line with what the VRMs output on the two boards.

Hmmm maybe something is pulling down the 5V line... at 4.7 you are already a bit below the expected range of many chips (usually 4.75 to 5.25). Do you also get 4.7V at the power or ISA connectors?

pshipkov wrote on 2023-01-17, 20:24:

The interesting part is that on one of the boards that voltage is 4.7V the other is 5.1V. These voltages are in line with what the VRMs output on the two boards.

Are you sure that 4.7 / 5.1V are at the VRM output? This would mean they overvolted the IBM 486BL3 CPU heavily.
Where did you measure the voltage? At C17 or at the ferrite inductor in the step-down circuit?