Make sure that your seat is not to low because a low seat will cause the quads to have to work hard.
I think that it just takes time for the body to adjust to exercise. You are probably growing new capillaries and blood vessels in the legs to bring in more nutrients and take away the waste products. I am thinking that in six more months that the soreness will be gone. During this time make sure that you don't over stress and injure the muscles.
If you are really concerned you could have a checkup to see if you have any circulation problems. Check and see if you feel a good pulse in the top of your foot.