Speedfan is only autoconfig for a certain list of mobo chip-sets any others have to be manually configured. Generally the health monitor software that (should) comes with the mobo (and of course its BIOS) should actually be reading the 12V port address while speedfan is obviously reading the 3.3V port address. But as Zap pointed out, if you want accurate voltage readings, you'll need to locate your test points and use a meter.
. Used to be that the 12V rail was only expected to have a +/- 10% precision as very few things in a system run directly on +12V (drive motors/fans/etc.) while everything else has local downward re-regulation and filtration. I guess maybe they have tightened the spec to +/- 5% as it is easier to achieve that now.
.bh.