I recently installed El Capitan through Clover on my Gigabyte GA-Z77X-UD3H LGA 1155 motherboard. I have updated and am now running 10.11.3, but at no point since installing El Capitan have all of my USB ports worked. I have 2 on the front of my tower that are recognized and work fine, but I have 6 via my motherboard on the back. Only 2 on the back work in OS X, 1 of which works 100% and the other is finicky. As for the other 4 on the back, I have tried various drives/keyboards/etc. to ensure that they don't work. My devices get power, but are not recognized within OS X.
Additional Info: All 8 of the ports are USB 3.0 with 2.0 compatibility. All of my devices work in any port when I boot my computer, up until I boot into OS X. In Clover Configurator, I have configured my system as an iMac13,2.
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