Now we're talking! I'm able to reproduce; it is timing dependent - basically you have to scroll up in the "dead zone" in the 2/3 of a second where there are no animations from 0:00.00 to 00:00.20 on the Map timeline to trigger this. It turns out it isn't a waypoint issue at all, but has to do with reversing a timeline when nothing is actively being animated.
I have a fix for the next version of Hype.
A workaround until then is to animate something in this timeframe; say have a dummy element with opacity 0% that just animates its left position.
Thanks for bearing with me!