You should see your doctor about the swelling and pain in your joints. Something is wrong. It could be as simple as taking an NSAID for the injury or something more complicated.
I know you just bought the treadmill but your body might need exercise that is lower weight-bearing, especially if you're trying to lose weight. The elliptical, bike, or swimming are all low or no-impact cardio activities that get the heart rate going without putting stress or strain on your joints.
Cut back on the running for a bit and go back to the walk/jog format you were previously doing (or even less jogging if you're experiencing a lot of pain). You can also just simply walk but raise the incline on the treadmill gradually - just don't hang on to the treadmill or hold on to the rails because doing so negates all the hard work you're trying to accomplish. Lower your center of gravity and pump your arms as if you were hiking up a steep incline. Trust me - it'll be a great workout without putting a lot of stress on your ankles like running does.