My particular test game is a native PC game (not emulated) from this year that runs at exactly 60 FPS. It is very light on CPU/GPU.
What you say about frame arrival seems a lot closer to the mark, but the skipping happens at set intervals (around every 5, 6 seconds) and lasts about 2-3 seconds. See my video a couple posts back.
Just to be certain, I ran a Genesis game with OpenEmu and tried recording tests with 59.94 FPS (native Genesis rate) and 60. Both exhibited the aforementioned behavior.