Even if your rails at the Molex look fine, they can be lower on the motherboard, especially near the CPU VRMs. This is due to resistance in the ATX wires, the resistance in the connector pins on the motherboard, and the motherboard's copper foil traces.
Then you have the invisible trouble maker which can hide behind very good looking voltages, be it at the molex or on the board, and that is voltage ripple...
As you load down a power supply rail, the voltage ripple (alternating voltage fluctuations sitting on top of the DC voltage) will increase... The ATX Specification states that for the 3.3V, 5V, -5V and 5VSB rails the ripple has to be 50mV or less, and for the 12V and -12V 120mV or less...
Aging power supplies, cheap power supplies, unusual cross loading situations or an overloaded power supply can cause the ripple on a rail to go way above spec and this will cause anything from random resets, sudden hangs (with or without graphical corruption) or BSODs/Kernel panics.
Just because your rail voltages seem fine doesn't mean they are, the only way to tell for sure is with an Oscilloscope on AC Couple and a vertical setting of 100mV or lower.