Without seeing the code, im sure it's because your gravity calculations depend on the framerate of the game, and since you have "more frames per time" when time is slowed, gravity acts way more in the duration of the jump.
You could just change the gravity depending on the timescale like:
if Engine.time_scale == 1:
gravity = 10
elif Engine.time_scale == 0.15:
gravity = 1.5