Obvious question but, are you sure your motherboard supports all 3 of those cards?

Most motherboards and even gaming motherboards will support one x16 PCIe slot and adding more cards either causes the main slot to degrade (i.e. instead of x16, you'd have x8 + x8). With 3 cards, it may be trying to segment out the bandwidth funky. Seeing that you are only seeing <10% output from the two additional cards that would about make sense. Also saying that you moved the slots around and noticed a difference could be the giveaway. Slot 1 is usually the primary 16x slot and the remainder might even be restricted to a x4 or x8.

Also, another obvious question, you didn't buy a cheap power supply right? Some of them, the wattage they say they are putting out isn't even close to what's actually coming out. The other issue is that crappy ones degrade over time (some faster than others). This can lead to power management issues with specific hardware that uses a lot of power (i.e. video cards).

I would try taking one card out and seeing if the performance increases.