you can NEVER....i mean NEVER!!! trust software for measuring voltages....ever
a DMM stands for digital multimeter, you can connect one to a molex connecter to measure 12V and 5V for the other rails i think you need to connect to the 20/24 pin cable going into the mobo..
Just to give an example of how bad software is for voltages, MBM (mother board monitor) said my 12V was @ 11.50......my DMM said 11.98