It could be a couple of reasons:
How old are your shoes that your're wearing? If you're going to run, your shoes must be new or newer. Yes, it will make a difference on your body. Especially,
running outside, you need all the cushioning you can get. Make sure you visit your local running store and they will fit you properly. There are different types of gates and your arches may not be hitting the correct spot in your shoes.
Another, it sounds as if you have "runners knee". You may want to google that and see if you have the symptoms. All you can do is RICE your knee. Running isn't made for everyone. Especially, if you are on the heavier side, it takes a toll on your body. I'm not saying you are heavy, just think about all the pounding your are putting on your body.
I, myself, was an avid runner (35-45 miles a week) for many years, up untill this past April. My knees can no longer take the pounding. I am a small frame women, so that will show you how hard it is on your joints (I have had a knee problems all my life). Grant it, I love the way it makes me feel, I still go for a run every now and then, but not everyday like I used to.
Finally, it could be your IT band. When you run or use the elliptical does it hurt all the up by your hip? The IT band runs from your knee to your hip. You need to stretch both before & after working out. Also, have you tried to ride the bike?
--Keep us posted
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