Hi there,
I'm running the GA-890FXA-UD5 Rev 2.1 with the F6 BIOS. I don't usually run the On-Board Realtek Sound chip but have enabled it and loaded the latest drivers from the Gigabyte website to see if I can help.
Sorry to report that on my board the Optical Out is working fine and I couldn't duplicate your problem.
However, the output signal from the Realtek Optical connection seemed quite low and I had to boost the input on my studios Minidisc Deck, that I was passing the signal through, quite a lot (over +12 Db) before I could hear it properly. This was with both Windows and Realtek's Mixer Outputs set to maximum.