I have a 4-port SYBA SI-PEX40062 card that I have been using in my unraid system for a couple of years without issue.  I just upgraded to an intel i7-6800k on a X99 motherboard and for some reason now only the drive on the first sata port of this card is detected.  I tested power and sata cables, even tried putting the card in a different slot, but no dice.  I had to resort to some older Sata cards I have lying around.

 

Any idea what could be causing this?

The obvious answer would be that the card is knackered. Have you tried it in another system?

There's a know issue with this controller and virtualization, never heard of only affecting some ports, but it can't hurt to try with vt-d disable.

Ok thanks for the advice.