I ran your sample (on Windows) and I don't see any stuttering, though the timings in the console log varies a lot, some are 1ms and some are 15 etc, but the actual animation seems smooth.
Not that I would be likely to notice anything wrong as the image moves so slowly and quickly goes off screen.
Window mode usually doesn't have perfect vsync, and often can't have perfect vsync (as it shares the sync with other apps). You have to go to exclusive fullscreen.
I have no idea how Linux drivers work, but as long as other games work correctly and you swap in fullscreen mode with time to spare until vsync I don't see why you would get stuttering.
Erik, thank you very much for running it on your system. I really appreciate the help.
I am definitely running in windowed mode, and I noticed when I went to fullscreen in Windows the problem almost completely disappears. In windowed mode though, the stutter can still be seen and this problem does not occur with other games. Your explanation of not being able to have perfect VSync makes sense though, thank you.
As for Linux though, it still does not explain why the stutter is so prevalent - and this is with glut or with SDL. It's like it takes the Windows problem and enhances it. And I have the latest drivers on 12.04 and on 13.04, but for 13.10 it is just rolled into the OS. I wonder if this happens on CentOS or another distro....
Still doesn't make sense to me why other games don't have the same problem, such as the Gish game. Same environment, with no apps running, etc.