My physical therapy brain is about to emerge. You've been warned. :)
As we age a lot of us lose stature due to postural changes due to arthrtis, bone abnormalties, actual bad posture (over time), poor body mechanics (over time), ETC! If you have arthritis in your knees (exacerbated by running) the cushioning you'd normally have in your knee joint could get work out quicker. I Dont like to buy in to that theory regarding running because well, I am biased as a runner. But most of my colleagues would disagree to my chagrin. Anyway, cartlidge wear done can cause height decrease. And depending on your arch, you could be becoming more bow legged as the cartlidge wears more on one side vs the other. That's why a lot of my total hip or knee joint replacement patients are actually taller following joint replacement. That surgery freaks me out as a runner yet I am around it all the time. Anyway, i would say unless extreme, your height decrease is probably normal. Also you are shorter at the end of the day the beginning due to gravity's compressive force . So be sure to measure in the AM =)