Ok, so warm reboot --> controller vanishes, but on a cold start, it's present. And the system does boot from it when it's detected, just not when it vanishes on a warm reboot, right?
Hmmm... what power supply are you using with that system, and what's the rest of the parts list? Have you tried the system with the Dual-Power System card removed? The reason I ask is partly because the DPS apparently increases the demand on the +12V line, and as ironic as it may sound, the DPS may be pulling so much 12V power that the other components are starving. Just a hunch. 😉
One person remarked that with his Gigabyte DPS-equipped motherboard, Gigabyte's tech support recommended switching to an Enermax PSU, even though he already had a good Antec TruePower unit, and this solved the problem. This is interesting, because both are good-quality units but the Enermaxes typically have very high +12V amperage ratings, supporting my little theory about DPS.
So start by removing the DPS and perhaps reducing the electrical load on the system (unplug non-essential drives, lights and fans) and see if this changes the situation. Good luck, and welcome to the Forums eemain 😀