Bones Cracking, and Why?

I like to crackle knuckles always have so forgive me.  I am a nurse does not mean any thing as this is not my area.  Years ago when I was in my early 30 s I saw PT about my knee as I was having problems as a runner I asked about my knee cracking and said it in such a way she said Thank You yes it normal I wish all my pt's say that as every one comes in complaining about their bones cracking.  Please do not think I am making less of your situation as I am simply sharing something it reminded me of when I read your post.  Now I am a case manager and I regularly run across something called crepitus which may or may not have any thing to do with your current situation.  I would follow up with your doc and try not to worry.  Wikepedia has a good description of crepitus again it may or may not be what is going on with you.

My joints crack all the the time (ankles, knees even hips). My ortho said it's totally normal and not harmful. 

http://www.livescience.com/4125-knuckles-crack-joints-creak.html

The concerto comes from the pop of gas bubbles escaping the joints, snapping tendons and ligaments, and rickety arthritic joints.  

Joints come in a variety of shapes and sizes. The pivot joint lets us say "No" with our heads, while the hinge joint lets us swing our elbows and knees like a door. A baseballpitcher uses the tremendous range of motion of the ball-and-socket joint in his shoulder to throw fastballs. And sliding joints in the backbone make gymnasts' backs so flexible.

Releasing gas

A protective fluid cushions most of the joints in our bodies.

Inside a capsule that safeguards bones connected at a joint, synovial fluid keeps the cartilage, tissues, and muscles lubricated and well nourished. Nutrients float inside the fluid, along with gases, such as oxygen, nitrogen and carbon dioxide.

As you bend your fingers, the joint capsule stretches. To make more room for the stretch, gases release out of the fluid. The pop of your knuckles is the sound of gas as it bubbles out of the fluid, scientists say. Before your knuckle can crack again, the fluid must reabsorb the gas.

More to it

Tendons and ligaments make a loud racket too.

Tendons are like rubber bands stretched over joints that keep muscles attached to bones. Similarly, ligaments extend to connect bones to other bones. Sometimes, tendons and ligaments slide out of their spot at the joint and then quickly snap back into place.

If your knee cracks when you stand up from sitting on the couch, you're likely hearing your tendons and ligaments popping into proper position around your knee's joints.

Arthritic joints not only cause pain, they can creak as well.

Connecting bones loose their smooth cartilage and grow spurs on their edges. The amount of synovial fluid also increases, making the joint feel stiff and sore.