I'd say file a bug report or just allow for some tolerance in your level design for the jump height. It's supposed to be framerate independent, and was in the times I've seen it tested before. Maybe it's something like the jump sustain that can't really be 100% framerate independent?
If it's really a nuisance you can try cramming dt in the y velocity somewhere and see if you can tune it to be more consistent. Two possible ideas are below. Just try different values of k starting at k=1 and see tuning that up or down does anything useful.
-500*k*dt or -500+k*dt