Interesting and good to know. I'm in a similar situation. I installed El Capitan on an available SSD, and I have another SSD that my windows install is on. I'd love to be able to boot either from Clover but when I replaced all the drives that were unplugged during the installation they were all taken, and seem to work fine. But the windows install... for 1.) isn't identified as being a boot drive, just a legacy drive. And for 2.) won't currently boot from clover. It will however boot from bios if chosen as the boot drive (seemly still running well too, even with the changed Bios settings. I would love to get these two drives set up to work in relative harmony without re-installing windows (if possible). Any guides you would be able to point out for that topic? Also, can I reset BIOs to optimized defaults? or do BIOs need to remain those settings for El Capitan to boot properly?