Look my post again, thank you.
Josecba - This is why the Internet is so frustrating. Your post is a copy & paste of outdated instructions and unless you've got some very strange hybrid of El Capitan betas upgraded to the release version:
It is no longer a matter of simply dragging & dropping two files and repairing permissions.
First of all, you can't just drag & drop piker's boot.efi files in place. You can sudo nouchg to delete the old one, but if you check ownership & permissions on the new one, they will not be -rw--r--r- root wheel as they need to be. Your system might boot with the wrong permissions, but - in my experience anyway, it won't be stable.
Second - There is no such thing as "repair permissions" in El Capitan. You can't repair permissions on an El Capitan installation from any version of OS X. The option is simply not available.
So what the hell are you saying? Can you drag and drop critical System files on an SIP system? Does your version of Disk Utility - from any OS - allow you to repair permissions on the El Capitan installation?
If so, please post some screenshots and describe your process in detail.
The current process of replacing the boot.efi files is considerably more involved than a simple drag & drop, repair permissions & reboot.
I read all about it and did a clean install of 10.11 yesterday. If you didn't install, boot into Recovery, disable SIP, reboot into recovery, manually fix permissions with chflags, chmod, chown, chflags, re-enable SIP, and then reboot;
Please explain it to me like I'm five and include some screenshots.
I don't see how you could have done what you say you did, especially the repair permissions part.