I've seen from other similar posts to mine that bent CPU pins might result in similar problems but we're mainly talking about systems built from scratch. In my case the system has not exhibited problems for nearly 3 years and it still works fine once POST completes so I very much doubt that is the problem.
Most likely there are no bent pins, correct. This step of taking photos would only be to make extra sure of that, since the CPU is out for the re-seat anyway.
You see, the CPU also houses the memory controller, hence the speculation that random CPU+DRAM LEDs may have to do with contact issues between the CPU and the 1718 tiny pins in the socket. How they can develop after three years? Beats me. But, there is no official explanation as to why this keeps happening on MSI AM5 600-series boards to a certain percentage of users. Small percentage, but still, we have a couple cases each month.
To me, there should be some kind of physical cause here, because sometimes it happens after the PC has been moved, or after the CPU cooler has been changed. Consequently, taking out the CPU and installing it again, letting the socket mechanism apply the torque properly and evenly again, might help in such a case. So regarding the physical things to try with the PC to solve it, this would be the most promising one to me.
I have zero experience of doing something like that! I'm happy to upgrade things like RAM and hard drives etc but that's about as far as it goes. I have considered building my own custom PC in the past but figured out that you can pretty much get someone else to do it for relatively little extra cost so decided it wasn't worth the risk.
We all started from zero at one point. Ok, way back in the day, when CPUs consumed 5W of power and had a tiny heatsink (if any) without a fan, and things were more robust, it was probably a bit easier to start messing with it. On the other hand, there was no internet, no Youtube videos explaining things, nothing.
But, yes, this is probably not the best task to start with. It seems you can reliably get the PC to POST now again? Was there ever another delay or being stuck on those LEDs?
Interestingly I've just flashed the bios to the latest 1.O2 version and this has resulted in the above settings reverting to defaults, is that supposed to happen? I haven't disconnected the battery so I'm puzzled. The battery is a brand new one btw
Yes, each BIOS update will reset the main settings to defaults. Only the fan settings are kept sometimes. Batteries last 5-10 years, no need to replace it prematurely unless it loses BIOS settings on each boot.
If you can boot normally now, we should just see how the case develops and not do much of anything. Yes, you can set DDR5-5600 manually, of course A-XMP would also set the timings to something tighter, which would improve performance. But if you want to stay more conservative now, set DDR5-5600.
The BIOS offers all the timings etc. of course, but you don't need to set them. I change maybe a quarter or less of the BIOS settings overall, the rest is good on defaults. It's also ok to only change a handful. The default settings can be too conservative sometimes, but at least they should be stable.