I believe those top 2 ports are from the Asmedia controller. Try the second bank of gray ports and make sure you're in AHCI mode. To be sure turn off the Asmedia controller in the bios.
The black SATA ports utilize RAID too, and that's where I would have put the HDDs and left SSD to native SATA3 port. I've almost always had issues with ASMedia ports on my Intel boards. It's why I went PCI-E to begin with.