I've done a video on something similar to this but here is a rundown on what I was encountering:
A 5200 sent in for services had a note stating that top fire button wouldn't work on the console. This is an issue I've run into before and in fact have created a video on it. It can be due to the controller having a broken trace of course on the flex circuit inside it. But... it can also very well be due to a faulty 4052 MUX chip inside the console located at U13 or A13 depending on the age of when your 5200 was made.
Well, that was indeed the same issue with this 5200. But after replacing that and confirming the top fire button was now functional again, I then used my port loopback tester board with the diagnostics and was surprised when a slew of other errors came across indicating issues with the keypad.
I then used a different program for just testing the controllers and sure enough, whenever you put a controller into port 2 and pressed the pause button, it would call the entire aux buttons to register all at once on both controller 2 and port 1 even though a controller wasn't plugged into port 1?! So that meant Start, Pause, and Reset were all registering at the same time. I later found out that when pressing the 4,5, or 6 buttons that it would also register ever single keypad button in that same column to also register. Obviously that wasn't going to do!
In testing the other ports, I found out that port 4 suffered similar issues but only the keypad section was messed up in that pressing 1,2, or 3 would cause all the keys on those columns to register at once. Very odd.
Diagnostics told me it was a keypad issue so that was good. I then went to the service manual proceeded to follow the flowcharts for what might be the issue. My 'hunch' was that one more of the other 4052s was having issues. However, the flowchart kept pointing me to either a faulty GTIA (Which does handle some of the keypad controls), bad GTIA socket, or a bad 7400 chip near the RAM section. So I tried replacements GTIAs and 74ls00 chips with no change. The flowcharts have you using an O'scope to check for activity on the various triggers lines and such. Well, I was seeing activity or pulsed indicating polling that the console is doing to check for buttons being pressed, but I was seeing something else odd as well. I was seeing what would appear to be ghost pulses between the normal square wave I should be seeing.
I proceeded to then use my multi-meter and checked all of the connection points from the GTIA to the passive components to the MUX chips to the controller ports looking for any shorts or broken traces. Everything was checking out... After hours of checking everything the flowcharts and schematics were telling me and nothing else to go on, I decided to something I should have done in the first place. Guess what that was?
I removed each of the 4052 MUX chips (Kinda a PITA since these were all soldered to the board and not in sockets). And checked each one of them in my Bitback chip tester pro. Sure enough, I found another failed 4052 at position U12 about middle of the board just ahead of the controller ports. After installing all new sockets and putting in the original 4052s that passed and replacing U12. Finally the controllers were working proplery again and the controller loop board was passing the diagnostics!
The moral here is that people are SO quick to blame the controllers on the 5200 for their woes. The reality, is that the 4052 MUX chips are very prone to ESD failure and fail they do...often. Especially the RCA branded ones.
Next time you have controllers issue with your 5200. Don't just assume that controller is a POS and blanket blame it. Have the console checked out to be sure it isn't something internal causing an issue.
The pic below shows the two 4052 MUX chips I had to replace to get this fully working again. They have little silver dots on them to indicate I replaced them and to make where pin 1 is. Again, they are highly prone to failure so if you own a 5200, best to have a full set of these on hand just in case. They are cheap ICs so it is good insurance to have on hand. In this case I have small stash of OEM RCA ones that have tested good that I've pulled from other dead 5200s over the years. I suspect in the past that U10's 4052 was changed out in the past as it was already in a socket and had a different lot number on it from the others.