The clicking could be due to a lot of things--what does your doctor say? Often, there is scar tissue that forms when you have an injury this severe--it is like big rubber bands, and can cause clicking, snapping, grinding, and so forth. There could be a chondral defect, or a place on the bone where the fracture occurred that did not heal completely smoothly (also called a chondral flap). It could just be that the muscles around your knee aren't back to full strength yet, and so your kneecap isn't tracking properly in its groove yet.
The point is that your doctor, who has been inside your knee, is the best one to help you figure out what's going on. If you can't see him/her, then what about a physical therapist to help assess your knee strength and tracking.
You may want to do some research on your condition. The cracking and popping you are feeling/hearing is called crepitus, and I believe it's pretty common after a fracture like yours.
Finally, check out the bone breaks around the knee section below--you are in very good company.
Heather
