Some motherboards have utilities provided by the manufacturer that can run under Windows. Tyan, for example, has a monitoring utility that supports a bunch of their motherboards.
What brand/model of motherboard is it? That might help somebody think of an alternate tool. A manufacturer provided tool is probably the most likely to interpret the sensor values the way they intended.
Speedfan typically detects a whole bunch of sensors, some of which are not really valid. It's possible it just needs to have different sensors enabled. I think it also has some way to add offsets to the readings. But of course in order to do that you'll need to find some more trusted readings inside Windows to compare with.
For voltages - motherboard sensors aren't really trustworthy. I would check them with a multimeter to see what the voltages really are. I've seen several boards where the voltage sensors were way off from reality. The easiest voltages to check are the +5V and +12V, which are on the 4pin molex drive connectors.
The onboard sensors are still useful though just for noticing whether the values are changing, even if their absolute reading might not be accurate.
The same inaccuracy is probably true for the temperature sensors, but it's not as easy to get a true reading of the temperature so you're more forced to trust what it says.