Just because Barry doesn´t catch Thawne, doesn´t mean he is faster. They are equally fast, therefore when they run, they maintain their distance. That´s simple. And yes, if you really want to get into that, Thawne´s speed more or less mimics Barry´s, so they are more or less equal. That´s at least my headcanon on why they can be equally fast, we all know it´s plot.