Lol. Yeah, welcome to the consumer world "accuracy". The A/D chips and the thermal diodes on your board are mass produced. To keep production costs of these chips (or atleast the cost of mass buying them) down they're pretty loose tolerances on both. PSU outputs can be called good by a manufacturer if within ±5-10% depending on the manufacturer and the grade (high or low $) of the PSU. I'd expect motherboard component's readings to be accurate within probably about the same tolerances. As long as the components on the motherboard do their job to regulate these voltages you wont notice a difference though.
Trust the volt meter.
What, did you find your 12V rail to really be like 11.45 and 5V to be something like 4.6?