I think the problem with mine (due to the crapness of my phone) is that it'll lose my position for a few minutes, and then try to catch me up when it regains GPS signal. It then calculates this leap forward must have happened at an enormous speed, and discounts it.
Anyway, i've only had one Pokemon run since the update, and caught pretty much everything else with 1-3 pokeballs, so i'm not sure about any perceived difficulty rises.