I don't think the HWMonitor voltages are right they look really whacked out to me plus the AID readings are completely different,
I would trust the bios if things are runninng right and your bench marks cause no errors, you might try uninstalling your apps and re-install make sure it's the latest version also maybe try some different apps, you could hook you PSU to a different board if you have access to one and get a reading the only other thing is get a PSU tester. And most importantly keep a close eye on things, I understand,that would bug me too
That's correct. My old 12v rail reading was 11.73 in the bios; ran my ps that way for years before even trying the hardware monitor software. My asus board has some accurate software that matches the bios dead on, but I don't use it. You might try searching your board manufacturer's website for some utility programs that monitor voltages, unless it's oem (hp, dell, etc).