You are entirely correct. Went to the Bios and it is Intel Matix Storage that is selected in the SATA Raid Option. I downloaded the software but it does not support 2012R2, only up to 2008.
Is there an easy way to swop to the LSI option without having to install the machine again? If you convert the drives to NON raid it will wipe the data, assuming it is the same if you change Raid controllers.