Have installed a Gigabyte GA-Z68XP-UD3 motherboard with an Intel Z68 chipset. On the Intel ports I was easily able to setup the Intel Smart Response SSD drive and hard drive as a boot drive combination. BUT - when thereafter installing a Highpoint RAID card the boot drive became unavailable and I had to break the ISR to find the boot drive again. I have seen discussions online on this incompatability but no answers as to how to "fix" it. Is there a way to have both ISR and a hardware RAID card coexist?
Compatibility problems between the Option ROMs of integrated RAID controllers and add in ones are common to happen.
In these particular cases we always recommend to update the system motherboard BIOS, update the firmware of the RAID controller and drives installed. If the issue persists you would need to address those compatibility issue directly with the motherboard manufacturer and the add in RAID controller itself.