video card? maybe you have dual graphics and TQAE uses the integrated one.. you can also try triple buffering

I'd say it has something to do with video settings. List your computer specs: OS, graphic card, CPU, RAM. It would be easier to help you to know these.

Well, I hate to necro this, but I am having the same issue. After 30 mins my eyes hurt and the game is unplayable.

Heres the DXDIAG report:
Time of this report: 11/19/2017, 12:19:44
Machine name: MSI
Machine Id: {EDF49442-FA87-4F76-AFD8-90B8492A877C}
Operating System: Windows 10 Home 64-bit (10.0, Build 16299) (16299.rs3_release.170928-1534)
Language: English (Regional Setting: English)
System Manufacturer: Micro-Star International Co., Ltd.
System Model: GT62VR 7RE
BIOS: E16L2IMS.302
Processor: Intel(R) Core(TM) i7-7820HK CPU @ 2.90GHz (8 CPUs), ~2.9GHz
Memory: 16384MB RAM
Available OS Memory: 16342MB RAM
Page File: 8655MB used, 10118MB available
Windows Dir: C:\WINDOWS
DirectX Version: DirectX 12
DX Setup Parameters: Not found
User DPI Setting: 120 DPI (125 percent)
System DPI Setting: 120 DPI (125 percent)
DWM DPI Scaling: UnKnown
Miracast: Available, with HDCP
Microsoft Graphics Hybrid: Not Supported
DxDiag Version: 10.00.16299.0015 64bit Unicode

Display:

Card name: NVIDIA GeForce GTX 1070
Manufacturer: NVIDIA
Chip type: GeForce GTX 1070
DAC type: Integrated RAMDAC
Device Type: Full Device
Device Key: Enum\PCI\VEN_10DE&DEV_1BE1&SUBSYS_11BC1462&REV_A1
Device Status: 0180200A [DN_DRIVER_LOADED|DN_STARTED|DN_DISABLEABLE|DN_NT_ENUMERATOR|DN_NT_DRIVER]
Device Problem Code: No Problem
Driver Problem Code: Unknown
Display Memory: 16259 MB
Dedicated Memory: 8089 MB
Shared Memory: 8170 MB
Current Mode: 1920 x 1080 (32 bit) (60Hz)

i had same problem and playing in windowed mode made it much better for me, just uncheck the full screen in video option

i find a solution at last! just go to the sceen settings from windows menu and find your monitor and then chenge the refresh rate to 144 from 60 that was default