I've got a system running Ubuntu 12.04 with an i3 2120T CPU/GPU. When I play video through mplayer, I notice when I'm hooked up to a screen via HDMI there is a small stutter (1-2 frames) every few seconds. I don't see this happening when I connect via DVI on the same screen. Resolution and refresh rate are same for both HDMI and DVI, so I'm not sure where else the problem could be coming from.
I've also tried two different screens, and different cables. I see the stutter with either HDMI-HDMI cables, or DVI-HDMI cable with DVI from the PC and HDMI into the screen. I don't see the stutter with DVI-DVI cables, or when I use HDMI-DVI cables with HDMI from the PC to DVI into the screen.
I've also tried using an AMD 5XXX series card with the open source radeon driver, and saw the same problem. I then tried an nVidia GeForce 210 card with the closed source driver, and the stutter went away. To me this smells like a driver/mesa/glx issue (since the problem went away with the nvidia card/driver), but I have no idea how to track this down.