Look at this profile: http://mzl.la/1KET2tS The vsync markers are spaced fairly evenly, but the composites are all over the place. Sometimes there are two composites right after each other on each second vsync. Vladan has three monitors. The primary monitor has a refresh rate of 50Hz, the two external monitors have 59Hz. The problem was reproduced when the Firefox window was on one of the external monitors.
Hmm, this profile is very weird, even the vsyncs aren't very uniform. Can you try removing one of the monitors and seeing the minimal configuration? Does just adding a second monitor at all already cause the issue to occur? Or does this happen only with 3 monitors? If he has only one monitor, does the problem go away? What is he doing, it looks like it's just scrolling?
Let's follow up on this when Mason is in the office
Ahh yeah we looked at this in the office. The values we're getting back from the DWM are not uniform, hence we're not getting uniform values. IIRC, Chrome suffered the same issue, just not as poorly. IE uses WaitForVBlank, but we can't use that since we listen to vsync on a different thread than the painting thread.