I've had contact with Chucky. He said that the INT2 behaviour is not as designed on the latest build of DiagRom, ie there's a bug that needs fixing as I understand it. There's no INT2 changes so that I can't measure them checks out. But this shouldn't affect the test itself though.
Chucky asked me to measure the signal on the _E signal on the pin of the IC and not the pad (as it may have a problematic soldering joint). As you can see in the attached image, the signal looks fine.
Chucky is also stumped by the problem. I've ordered 4 more CIAs and smd PLCC sockets that should arrive somewhere next week. I'll swap out the CIAs and see if that resolves the issue.
I've done more measurements and communication seems fine, I've looked at the _E, _W and _CIA_ODD chip select lines with two channels triggering on _W and _cia_odd and all seem as it should and there's no observable difference between CIA odd or even.
I haven't done any measurements with more channels, I've soldered on wires to break out the signals. I've ordered some micro probe clips to make it easier for more fault finding with 4 channels. I really feel the need for a logic analyser right now, because I can then record a few seconds and see what's going on exactly. Maybe one day
I've checked if the CS lines of odd and even are enabled at the same time for example, which wasn't the case either. I was thinking maybe two devices are active at the same time giving read errors.
I've experimented with shorted address and data pins on purpose, the machine would crash immediately so there shouldn't be any short if the machine doesn't crash. I noticed that the CIA_ODD is on different address lines compared to CIA_EVEN, that's the only real difference that could be common between two chips being swapped. But so far I haven't found anything that could indicate a problem.
The only difference is that when it reads from the TOD register the values are not as expected. It could be a localized fault within that register under a certain configuration. Also, I may have made a mistake in swapping them while thinking it was swapped but it actually wasn't. Since they are soldered to the board now swapping them is a hassle so I'll wait for the sockets to arrive.
I do have an Amiga 500, but I don't have diagrom for that. But I could take some measurements with Amiga test kit active.
I'm not sure if it's significant, but the printed text on what now is the odd cia is partially wiped off. All I did was use a cotton swab with 99% alcohol on it to clean flux off. It could be a much older IC than the other one I have, which is also printed much clearer. I bought one from ebay and the other as NOS from amibay. Maybe the ebay one was from a questionable source. The other 4 on order also come from amibay as well (same source). Maybe there's different revisions floating on the internet.
I'll let you know when the new CIAs arrive and tested on the ReAmiga build.