Can't you go into BIOS when you have the RAM modules only in 1st and 3rd slot?
You should verify that the BIOS update went down successfully by looking at version number. Does it say it's the latest?
Have you seen this on http://www.gigabyte.com/products/product-page.aspx?pid=3809&dl=1#
(Note 2) To reach DDR3 1800MHz or above, you must install two memory modules and install them in the DDR3_3 and DDR3_4 memory sockets.
I'm not sure, how it's related to you, just thought I mention it.
Now let's try to find out about that beep code.http://download.gigabyte.eu/FileList/Manual/mb_manual_ga-880gm-usb3_v.3.x_e.pdf
Q: What do the beeps emitted during the POST mean?
A: The following Award BIOS beep code descriptions may help you identify possible computer problems.
(For reference only.)
1 short: System boots successfully
2 short: CMOS setting error
1 long, 1 short: Memory or motherboard error
1 long, 2 short: Monitor or graphics card error
1 long, 3 short: Keyboard error
1 long, 9 short: BIOS ROM error
Continuous long beeps: Graphics card not inserted properly
Continuous short beeps: Power error
Does it say anything to you?