Disk Errors on both Motherboard SATA connection and on HBA connections

My understanding is it is specifically for the SATA controller. You need to use something like storcli, sas2ircu, or lsiutil for the SAS controller. I think storcli will work for you. This thread may help or give other ideas, but I think (?) part of the difference there was they were dealing with the onboard SAS3008, not a discrete HBA.