Ok, this is the final fix to #93 (closed). Particles are not allowed to move to a longer time-step unless we are currently doing a time-step of that size. That will prevent particles from being completely all over the place in the time-step hierarchy.
It wasn't physically wrong until now, just not efficient and very confusing.
With this fix in place, there will always be a time-step every so often where all particles are updated.