What motherboard do you have? I think I have the exact same issue.
Edit: See now that you have a gigabyte Z87. I have an Asus Z87-A with the same problems.
I have Z87-A and also have problems with my USB 3.0 ports. My USB 3.0 external drive has to be connected to USB 2.0 to work, but USB 2.0 devices work fine in the 3.0 ports. This is the only issue I have with El Capitan as of now.
I also have some problems with my USB ports. The USB 3.0 ports are working, but my mouse which is connected to one of them stops randomly for a second or two and my external drive isn't working at all on USB 3.0. USB 2.0 ports are working fine.
Hey. I've gotten my Hackintosh successfully installed and using the Clover bootmenu. After hours of searching I haven't been able to fix my last problem as of yet. What you see in these pictures are what my bootloader looks like now:
The option on the right is for my new Hackintosh...
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