I have UD3, 2600k, diff gpu/hdds but had no such issue... however there is a problem where it randomly reboot loops or gets stuck on the black part where the BIOS checks optical drive and says "loading operating system" (having a usb flash card plugged in makes this issue worse).
I think one of your new hardware is probably bad, even though the board clearly has some BIOS flaws related to SATA that has nothing to do with the defective chipset. Ports 0,1 are unaffected by the design flaw, and the flaw shouldn't affect brand new boards at all - the failure is gradual.