Right, bit of a strange one. I've been running clover without issues for about 2 years. Previously I was on 2953 running yosemite. I updated through the app store to el capital gm and updated clover to 3270 in preparation for the first boot under el cap.
Upon reboot I was met with the 'Bios like' screen with 5 options, the first being continue meaning clover couldn't find BOOTX64.efi. I've always had clover installed in / of Macintosh HD but thought I'd copy the EFI folder to the EFI partition disk0s1. Great, now I have the boot loader GUI back but I can only see Recovery HD, no Macintosh HD.
Weird, so I formatted and installed from scratch (I only need fakesmc, realtek81xx and my dsdt so its not particularly painful). I can now boot into el cap using clover on usb, installed clover to the hard drive and I'm back to square 1. I can't see Macintosh HD through clover. Is there an issue with build 3270? I'm doing nothing any differently to previous installs.