Unfortunately with the removal of the USB3 PCI I had the same issue. The strange this is if I boot with the stick and reinstall the drivers, after the reboot is OK. Then If I reboot again 50/50 chances to not have black screen.
Thank you for you suggestion. I’m suspecting a conflict with a usb 3 card (Highpoint 1022C) that I have installed lately although is working as it should. I’ll try to uninstall it. It’s a PCI 2.0 board, and maybe is conflicting with nvidia. Who knows.
Mobo: Gigabyte X58-UD7
OS: El Capitan 10.11.6
GPU: GTX 980
A very stable system without any reason started having random black screens on boot. Nothing changed. If happened the only way is to boot with usb stick and reinstall nvidia drivers. This fixes the problem for the next...