Hehe, rescued from dead bottom.
When you test with a multimeter, you're getting the actual voltages that the power supply is puting out, but not necessarily what the motherboard is getting. Remember that the psu's juice is passing through tons of components and connectors on it's way through a motherboard, all of which will drop voltages slightly just by resistence (no superconductors on a motherboard yet).
Software programs tend to see more closer to what the motherboard is getting at the component level, though honestly, some aren't reading right or don't have software updates for current chipsets, cause I get some super funky readings on my AT7 (like around -7 volts for my +3.3).
Now if you have a large difference between them, and the software seems not be the problem, then look first at your power connector to make sure it's clean and not charred or melted.
Anymore problems, post 'em here.