Have you tested it under various 'dummy loads'? A common mistake among new developers is to assume that their unstrained A-grade system is a good benchmark for load sensitive coding. (system load being the primary cause for lag)
Oh true, I haven't really. It was a 48 hour jam game so no time for such things. Everything movement wise should be synced to framerate but there can indeed be a slip up there somewhere.
I wouldn't really consider myself a new developer, been programming since the early 90s.
I've just switched to a different computer and it seems that the problem isn't timing, but the game having jumps that depend on a too infrequently occurring collision glitch boosting it.