If the meter reads correctly, then the voltages are fine and the motherboard is just reading them wrong. If the meter reads wrongly, then there's probably a problem with the power supply, though seeing as the 12V line reads zero, the motherboard is obviously reading it incorrectly or else your computer would not be running...
Also, like Matthias said, modern computers do not use -5 and -12 lines. If switching supplies have no load, they can do goofy things, but since they're not used, there is no need to concern yourself.