Were each of those tests done while in full-screen mode? Again, the Windows DWM seems to give a higher priority to full-screen apps. Speaking of priority, have you tried adjusting the Synthesia.exe process's priority to something like "High"? I haven't experimented with that much, but I don't suppose it could hurt.
Otherwise, some intermittent hiccups are still the fault of our own code. A lot of the deeper underlying assumptions of the play screen were made over twelve years ago, just a couple years after I was getting out of college and didn't know much better. It has only been in recent years that
I've learned much of the programming style taught in schools (
OOP) isn't the right answer for the near-realtime environment of 60Hz+ graphics apps. We've slowly been making strides in this area -- a little in every release -- so hopefully those sorts of inefficiencies will be fewer as time goes on.
(I actually keep a small, hand-written Post-It note copy of
this tweet stuck to the side of my Synthesia dev machine's monitor.)