I ran into this issue as well with Unity 5.5.0f3. As stated above, the problem is specific to quitting the application while in DX11 fullscreen exclusive mode. I was using the native resolution, 1080p. Killing the process seems to be a viable workaround. Thanks to Sam for mentioning that. Here’s some DXDiag info in case it helps:
Time of this report: 12/21/2016, 14:59:20
Operating System: Windows 10 Pro 64-bit (10.0, Build 14393)
Language: English (Regional Setting: English)
Processor: Intel(R) Core™ i7-5820K CPU @ 3.30GHz (12 CPUs), ~2.9GHz
Memory: 16384MB RAM
DirectX Version: DirectX 12
Card name: NVIDIA GeForce GTX 980
Display Memory: 12203 MB
Dedicated Memory: 4060 MB
Shared Memory: 8142 MB
Current Mode: 1920 x 1080 (32 bit) (60Hz)
Native Mode: 1920 x 1080(p) (60.000Hz)
Output Type: HDMI
Driver File Version: 21.21.0013.7609 (English)
Driver Version: 21.21.13.7609
DDI Version: 12
Feature Levels: 12_1,12_0,11_1,11_0,10_1,10_0,9_3,9_2,9_1
Driver Model: WDDM 2.1
Graphics Preemption: DMA
Compute Preemption: DMA
Miracast: Not Supported by Graphics driver
Hybrid Graphics GPU: Not Supported
Power P-states: Not Supported
Driver Attributes: Final Retail
Driver Date/Size: 11/23/2016 4:00:00 PM, 17590064 bytes