Wiring is sperfectly all right. Otherwise the reader wouldn't be functional at all. I made it clear in the initial post that if you start the system with the reader disconnected and plug it after the OS is fully loaded, it is recognized and it works as expected/designed.
I contacted the local Gigabyte tech support and was adviced to return my MB to a retailer. Since waiting three weeks didn't seem sexy at all, I bought a new MB: AsRock 970 Extreme4. The reader works like a charm - no problems booting and overall booting time seems much faster plus no problem with entering BIOS (it was horrible with GA-970A-UD3 ). As you can clearly see, this is obviously some issue with Gigabyte BIOS programming or/and a defective board.