I noticed that too. I'm not sure if there's a better way to do it or not; as a piano player myself, it might seem more intuitive to me to have a visual indicator at each beat in the measure, and then just highlight each note (via color or something) as it's played. I think the reason it seems off is because it's so irregular, even though it does match with the music itself.

Kudos though, Etude looks great.

I'd suggest a combination of both mcav and cpr's suggestions. Highlight the notes themselves instead of the area around them. Drop the jumpy marker and replace it with a smoothly moving, constant speed vertical marker. It's a commonly recognized and understood element (used in pretty much any and every audio production / recording software). It also gives the viewer a better sense of the tempo. Remember, tempo can change drastically over the course of a song; the current marker doesn't demonstrate the difference between playing shorter notes at a slower tempo and longer notes at a faster tempo.

Maybe have a constant-speed thin vertical cursor along with (behind) the jerky highlight? That would help to smooth things out and get out of the "valley."

Or you could just highlight the current bar.