I noticed that Speedfan reads the +12V rail as 4.75 to about 5 V while on idle. On full load (during stress test) it jumps back to normal 11.89 to about 12.49 V. Got the same exact readings on CPUID Hardware Monitor and Everest.
I have tried two power supplies, Kingwin LZG-1000 and Sparkle 1000 W, and the results are the same.
If both power supplies are functioning correctly, then could it be my motherboard on the 20+4 pin or the 8 pin EPS?
I wouldn't trust Speedfan, if your system is stable then nothing should be wrong.
Software readings (Especially speedfan) do sometimes give inaccurate readouts, try using a multimeter if you really want to find out the voltages.