I am looking for some suggestions of things to try in order to diagnose a bad motherboard that gives a beep code error during POST. In particular, if I have an identical working board, can running the two side by side or other types of comparisons help me zero in on the problem?

Some details: These are laptop MB's with soldered CPU/GPU. The bad board's error code is six beeps a few seconds after turning on the machine, which then repeats every 10 seconds or so, and this is an AMI bios. At least, I think it is six beeps...they come in two groups of 3 each. I inspected the bad board by sight, and there is no visible damage to any of the components. I also tested most capacitors for a short circuit thinking that this might be an issue, but did not find any. The only way to have something different happen is to take out all the RAM; in that case, there is a single long beep.

Any suggestions would be appreciated.

 

The beep codes are stated on the internet..
https://www.lifewire.com/amibios-beep-codes-2624543

Personally I don't waste time trying to troubleshoot a motherboard as they are too cheap to mess with.. Trash and buy a new one..
I will give a quick visual inspection to look for any clearly visible issues but other than that its not worth the time...

 

In particular, if I have an identical working board, can running the two side by side or other types of comparisons help me zero in on the problem?

I doubt that having another board will be helpful. If you managed to isolate a suspected defective component and replace it; without being able to run diagnostics that exercised all of the circuitry, you could never be certain that you actually fixed all of the problems.

Case in point. I have a Tektronix digital oscilloscope plug-in for my 7000 series mainframes. Each time it's powered up, it runs a self test and can display error codes for any defective components. The problem is that it doesn't cover everything and I found at least one piece of hardware that isn't tested during the self test.

 

Trash and buy a new one..

This is a Zotac mini-pc MB, they're not manufactured any more. The only alternative to fixing is to trash the PC.

The beep codes are stated on the internet..
https://www.lifewire.com/amibios-beep-codes-2624543

So, I saw that and it resolves 6 beeps to a keyboard controller issue. But are there standalone keyboard controllers on modern boards? Aside from the CPU chip, all I'm seeing is a SuperIO chip, and a few random tiny IC's for audio, HDMI, etc.

 

But are there standalone keyboard controllers on modern boards?

That functionality is now included in the Southbridge.

Image courtesy Wikipedia:
https://en.wikipedia.org/wiki/Southbridge_(computing)

 

That functionality is now included in the Southbridge.

So based on this topology, and the beep code, the issue with the MB must be related to either the SuperIO chip, or the LPC bus connecting the chip to the CPU? Any other possibilities?

Btw, my CPU looks like this: