I think you are carrying too much. If you carry more than 40kg, when you run (not sprint, just run) your stamina (the long needle gauge) will drop. So if you are over-encumbered and stamina is low, you'll have to stand still and wait for a few seconds for stamina to go back up before you can run again. So watch out for your weight :) It's shown at bottom of inventory. later I'll add a warning circle that shows near the bleeding warning when you carry too much weight.