If you set UEFI or disable CSM then by definition you have to be absolutely certain that every piece of gear you have is compatible with UEFI version in the system. It seems that SSDs and certainly optical drive are not entirely/at all compatible. The thing is that some stuff like optical drives is so old that UEFI is often too much to hope for. I can recall examples on older chipsets when was running drives of motherboard in AHCI mode and DVD drives always behaved in a strange ways. Problem disappeared when I switched back to IDE mode. Don't, just don't, disable Legacy support for storage unless you're 101% sure. Out of curiosity have you tried to put BR drive in external enclosure and connect it with USB? Myself decided sometime ago that external optical drive is better for my health as I avoid issues with AHCI and UEFI (Windows protected mode insulates external optical drive from BIOS).
 
I've noticed on images above that you have PCI-SSD in last slot. I know that inevitably you'll lose coveted x16/x16 setup (which differs from x16/x8 or x8/x8 by nil - 0% in performance) but try and put the drive in that X4 slot for testing purposes at least. I've noticed on my own system that Gen.2 AIC work properly in x4 slot and show some quirky behavior if put in Gen.3 slot unless you set manually to Gen.2 (perfect example of not properly working lane negotiation). Lanes on x4 slot are drawn from PCH not from CPU and at least that part works as it should on Classy.

I just disabled hot plug on all SATA ports. I'll be re-installing Windows 7 UEFI later on and see if my drives are recognized.

Hmm hot-plug functionality is essential part of AHCI protocol or RAID... Don't want to spread doom&gloom, but it may be the reason behind not recognized array; in particular if everything is in Legacy mode.
 
Is array detected by BIOS or not? 

Did you perform a backup of data on array? If yes then try simplest of solutions: dismantle array and then recreate and re-initialize. The only thing which springs to mind is (corrupted?) meta-data written by chipset-RAID which Windows cannot process when you went from UEFI to Legacy. To remove old meta data the only way is to dismantle array, reformat each drive as IDE/AHCI and then again re-create array from scratch. 
 
It's really puzzling why Legacy array is not detected by Winblows in Legacy mode.  

Good to hear. :)
 
That's the problem with on-board chipset soft-RAID. Any major change in way how system boots may require re-doing everything. RAID AICs do not have this problem.