Found a solution, couldn't find the original link where I found it though.
It requires using RivaTuner.
You can download RivaTuner here
Note: I'm a nvidia user so I'm not too sure if this can extend to integrated graphics users and/or ATI.
Go to OpenGL Settings under Driver Settings in the Main Rivatuner window.
Under the Back / depth buffering tab, change the Back buffer flipping mode from "Auto select" to "Block transfer".
Tbh, I have no idea what this does but it got rid of the horizontal lines when running OpenGL games fullscreen.
Let me know if this made a difference for anyone.
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