it should be in seconds - the problem is that the paper assumes that the 'great circle' (straight line) distance between two points should be almost the same as the 'route' distance between those points, with an exponential probability distribution.
This means that if the path between two points is not simple (around a corner) the probability drops off very quickly. If the time between measurements is in minutes, this heuristic is pretty useless (and you should really use log-scale for your numbers!)
edit: this is actually shown in figure 8 of the paper where they explore different 'sampling periods'
edit 2: I have not explored other methods yet, but it would probably make sense to start by deriving the formula the way they do, by exploring ground-truth data.
edit 3: I just noticed that my comments are largely repeating what you're saying - sorry!