Cracking your knuckles is not bad for your fingers or joints. Inside the joints between the bones there is synovial fluid. In this fluid are tiny bubbles of carbon dioxide that expand or pop when you twist the joint, expanding the space containing the fluid. The reason the first crack is the loudest is because the CO2 bubble has had time to reform in the joint. As you keep cracking and the bubbles pop into smaller bubbles, the strength of the "knuckle crack" decreases. Thats why. if you keep trying to crack the same knuckle eventually it will stop working until you "rest it" for a while. The CO2 bubbles need time to reform.
Anyway, like any habit, its fun to do. Whether it's cause we like the feel of it, we like the sound of it, or because we like people's reaction's to it. We even try to do it when our body wont let us (ie when we have already cracked the knuckles until they quit cracking). Sometimes people can try to crack harder by twisting and contorting the finger joints in unhealthy ways, putting serious stress on the joint.
My guess is that this is what's going on. Over years, you have put stress on the connective tissue surrounding the joint by pressing on your finger, trying to get that extra crack out of your knuckle (when the CO2 bubbles needed time to reform). My advice is to continue to crack your knuckles happily, with the knowledge that its not at all bad for you; however, I do add this caveat, once your knuckles wont pop anymore, dont force them. Your finger pain should resolve in no time!