I understand that when you have the boot optimization on the system is not able to boot from your array.
The problem that you are experiencing may be caused by the spin-up time of your hard drives. Remember that the hard drives need to be ready before the controller tries to read them.
If your hard drives require a lot of time to become ready, you may encounter this problem.
You can try to get in the BIOS and under the configuration tab, SATA configuration there is an option called hard drive pre delay, change this to 3 and try to boot.