So there is none of them in the Device Manager whatsoever ?!
Make sure you are using latest BIOS (F8a for versions 1.x).
Switch to AHCI and see what happens or if it s AHCI now switch to IDE Mode.
Try different SATA cables as well.
I have encountered performance issues with those 2 ports myself with the same board version 1.0 and stopped using them , but they were working with XP.W7 and some Linux distroes.They were working in multiword instead of UltraDMA