All motherboard fan leads stopped working except CPU1?

I have a year old system built on an MSI x99a motherboard, using a Asetek 550LC 120mm liquid system as the main cooler. The pump was connected to CPU Fan 1, while the radiator fan was on SYS fan 1.

Recently, the computer started overheating, and after a little investigation I could see that the radiator fan was no longer spinning. I've tried swapping it with another identical fan, and connecting it to the other leads (SYS 2 and 3, and CPU 2).

Neither the BIOS or any in-OS fan control software recognizes anything aside from the CPU 1 connection (which shows as a fan although I assume this RPM reading is for the pump?). They all simply show as 0 RPM and setting them to manual or auto doesn't change anything. The pump sounds like it's functioning (and the radiator heats up quickly)

Any clue as to why this would happen? I had done some cleaning with compressed air that could have loosened leads, but at this point I've tried 2 fans in 4 different leads, so a loose connection seems unlikely. It simply seems like the BIOS / mobo no longer is powering on anything but the CPU 1 connection.

Any ideas?