J.F.
I'm assuming your doctor is concerned about Melanoma. Birthmarks with an irregular border, irregular/odd shape, color variations, and ones that grow rapidly in size are all symptoms of skin cancer. Melanoma is the most harmful skin cancer, but it's also got a very high treatment rate when caught early.
I don't mean to worry you. I honestly don't know that much on the subject, but this is the first thing that came to my mind, as I too have birthmarks the doctors have been keeping an eye on all my life. Melanoma was always their explanation for the concern. I'd call his doctor and make an appointment. If you're not satisfied with the answer you get, see a different doctor for a second opinion.
The other thing that comes to my mind is, has he gone through a growth spurt lately? If he's gained a lot of height/weight from growing (this happened to my brother) his skin will stretch rapidly, and the birthmark won't have time to grow with him, it will just get pulled and stretched out of shape. This will cause it to look radically different than before. We took my brother in when he was about 4-5 with this same concern. (his is on his calf) The doctors ran a few tests and found out everything was fine, he was just growing like a weed. Now that I think about it, I'm betting this is what's going on with your little guy, but I'd still call his doctor, just to get a definite answer and put your mind at ease. I hope all goes well. :)