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.
Games affected:
- Doom 3
- Star Wars JK II Jedi Outcast
- Star Wars JK Jedi Academy
- Return to Castle Wolfenstein