Mystery CPU Diagnostic Light

That's what I originally thought as well but according to this guide on page 33, it's not the case. Both lights are on, actually which leads me to believe something is up with both CPUs, but the thing actually booting up tells me otherwise. I might pop the old Nehalems back in when I have a moment and see if that changes anything.

http://tim.id.au/laptops/apple/macpro/macpro_early2009.pdf

Oddly enough I did have an error symbol on one of the slots in "About this Mac" immediately after installing the RAM. I moved the cards around and it went away.

Alright, quick update. I did a bit of troubleshooting with the CPUs. Swapped both A and B; both lights still persist and the machine boots fine like before. I then swapped the X5680s out for the old E5520s that I replaced but that made no difference as well.

Someone on iFixit that I posted the same question to actually said the CPU lights being on may be in regards to an EFI error that could be related to the 4,1 -> 5,1 flash I performed. Since the CPUs seem fine, that may be the likely culprit but we'll see. I have yet to hear back as far as what I should do next. As far I I know, it it sounds like I may have to roll back the flash and attempt it again.

Processors are delidded, so no fitment issues there. The heatsinks seem fine as well, the fans in them are running and there isn't any sort of play in them once they're tightened down. At this point I'm kind of at a loss. This issue only cropped up after I installed the new CPUs following the firmware update. I'm doubtful that the entire riser board is bad as there was no problem prior to the CPU installation.

Taking DIMMs out didn't change anything, and there isn't any visible symptoms once I'm booted up and running. I'm just throwing ideas out at this point but is there a possibility this could be power related? This all feels like some weird fluke.

Worst case scenario, since I'm not planning on keeping this rig I'll just try the reflash(which as you mentioned probably won't do anything) and assuming that nothing changes I'll just cut my losses and hope for better luck on the next one. This is only my second 2009 build so I've still got a few things to learn when it comes down to troubleshooting.