I have an R610 that has stopped discovering drives on boot. It was previously working. I've done my fair share of troubleshooting and none of the diagnostics show up any errors. Both A and B cables are properly connected from the raid controller to the backplane. The odd thing is, though, if I move the raid controller from the designated I/O PCI slot into the other PCI slot on the riser, everything works as it should. I thought the riser may be the issue so I bought another one and it changed nothing. I would like to see if anyone else has any thoughts on this before I go through and replace every part along the way trying to chase the problem.
Based on what you're saying, I'd replace the motherboard. Moving the controller proved it was good. It's not likely (though still possible) that you have 2 bad risers, but I'd be looking at the motherboard. I'd be expecting any number of stability problems if the proc were failing.