The voltages that you are referring to are called "signaling voltages." This is the voltage signal that the motherboard and video card send to each other so that they know they are compatible. They are 3.3V (original AGP/2x), 1.5V (4x) and .8 (8x). You shouldn't have to worry about the signaling voltage, because if the card fits in the slot, then it will work on that motherboard. Each AGP slot is notched in a different way so that you can't fit an 8x card into a 2x slot.
The AGP slot on the "new" motherboard could be bad, or you might be having an issue setting up the new board. The new motherboard might even have a good AGP slot, but a bad memory slot or a broken CPU socket. Try getting it to run with an old PCI card. If that fails, then return the new motherboard.