Don't worry I had the same issue but after carefully reading the important steps and settings here: https://www.gigabyte.com/MicroSite/462/mining.html I managed to get it to work. Think the setting that caused issue was Compatibility Support Module (CSM) option. It says to have 'Disabled' but from memory I had to have it 'Enabled' before my 60GB SATAII  SSD would boot Windows.

The other important steps to follow, some already suggested were:
1. Update BIOS - latest version 25a here: https://www.gigabyte.com/Motherboard/GA-H110-D3A-rev-10#support-dl
2. Change “Max Link Speed” setting from “Auto” to “Gen2” (M.I.T / Miscellaneous Settings / Max Link Speed)
3. Enable Mining Mode (Peripherals)
4. Change "Initial Display Output" setting from "PCIe Slot1" to "IGFX" (Peripherals) - initially I wasn't using on board graphics but seems best option to free up resources.
5. Change “Above 4G Decoding” setting from “Disabled" to “Enabled” if needed (Peripherals) - I have GTX 1070's with 8GB vram soof course I enabled this feature.
6. Windows Update turned off is recommended - I went one step further and ran Spybot Anti-Beacon link: https://www.safer-networking.org/2016/anti-beacon-1-6-available/
7. Go to Control Panel / System and Security / Power Options and select "Choose what the power buttons do". Click "Change settings that are currently unavailable" and disable the "turn on fast startup (recommended)" function.

Also wanted to mention the ability to run a 7th riser on the M.2 slot isn't supported on this model for those considering it. Chart clearly says 6*PCI-E only. If you're considering purchasing this motherboard I can't fault it like OP, although I think like anything it takes patience and doing some research before jumping to conclusions. Here's an interesting review link: http://1stminingrig.com/gigabyte-ga-h110-d3a-review-the-new-best-motherboard-for-mining/ Note down the bottom there are also comments about people overcoming similar issues.