This could be a kidney stone ( I've had three so I know what Im talking about ) the resone this could only happen when you run is that when you are bouncing along, the stone is scraping you Ureta ( the tube that connects your bladder to your kidney ) so hence the blood.
Do you feel sick or have dull pain in your left or right flank, get this seen to immediately, kidney stones are horrendous the pain is more painful than childbirth according to women who have given birth and had kidney stones.
I had them and I wanted to kill myself, the pain is nothing like I've experience before and let me tell you I'm ex-army so I've experienced some pain LOL( shin splints, running on burst blisters for another 12 miles LOL )
Seriously though get checked out xxx