So your window/view/app surface/GUI are all 1280x768, but your display size is 1366 x 768
This means if you run the game full screen mode, the game is being stretched by a non-integer amount horizontally, unless you have the Keep Aspect Ratio option ticked in your graphics settings.
This will stretch the pixels unevenly, which causes the black lines is my guess, but I could be wrong. The reason I say I could be wrong is that you said you don't get the lines when you make your game 640x360, but this is also not evenly scaling into 1366x768.
Are running the game in full screen mode?
What happens if you run the game in windowed mode, do you still get the lines?
What are your graphics options settings?