3ware raid controller does not get a proper reset signal after a reboot

I have a linux server that has a 3ware controller 9650SE-4LPML connected.
Today, I migrated this server with all its disks and raid controller to a new motherboard + cpu + ram (gpu is also changed).

The process was smooth apart from one repetitive problem; when I reboot the server, the 3ware controller BIOS messages do not show up. I assume this means it has not been properly restarted. Instead of booting to the OS again, the Bios screen comes up. If I insert a bootable CD in the tray , the UEFI will try to boot from the CD (even though it is not 1st in boot order).

Since a Major difference is that UEFI initialises the new hardware (while BIOS initialised the old hardware), I feel that I need to tweak some UEFI value to get proper reset signal , but going through UEFI did not give any hints.

note that powering off and then on allows for proper initialisation of the raid controller and thus the system boots fine. It is important to be able to reboot it too however.

EDIT:
old motherboard was asus P5Q Pro, new is Asus Z87-K rev 1.04
old cpu was Intel core 2 duo, newer is a Intel core i7

Answer

Attribution
Source : Link , Question Author : nass , Answer Author : nass