This is a fairly common problem called Chondromalacia patella, or chondro for short. Basically the cartilage underneath your kneecap has become rough over time due to a unnatural gliding of your kneecap against the condyles of your femur.
Now before you get ready to jab a scope into your knee you should know that there are a couple of types of cartilage in your knee. There is the meniscus which is the shock absorber that sits between your tibia and your femur. There is also articular cartilage, which covers and protects joints.
Think of the cartilage on your knee as a paved road. Over time you have developed some pot holes. When you drive over a smooth road, you don?t notice anything. When you drive over a road with imperfections in the surface it can be an uncomfortable ride.
Pain will usually occur with squatting motion, climbing stairs, and sometimes after a period of inactivity (long drive, watching a movie).
The good news is that most everyone has some degree of chondro, some worse than others. Typically chondro is caused by a weak VMO (vastus medialis oblique) or the tear drop muscle in your quad. The knee cap is kind of like the rope in a tug of war. There is a constant battle going on in your knee between the VMO and the vastus lateralis.
There should be a distinct firing pattern of your quads beginning with the VMO and the other 3 muscles following suit. The VMO is strong, but lazy if the VL fires before the VMO its not strong enough to battle the rope back to the middle and the kneecap slides toward the outside of you leg. If the VMO fires at the same time or slightly before the VL then there is a standoff resulting in the kneecap tracking in the groove of the condyles like it should.
Sometimes there are flexibility issues involved as well. Watch out for a tight IT Band and hamstrings, as they are often culprits of a poorly tracking patella.
If there is no pain associated with the crunching be aware that you have the problem, and should begin to try and prevent any further rubbing.
Focus on VMO strengthening, stretch your hammies, and IT band. Severe cases can benefit from McConnell Taping to help unload the VMO and re-educate it.
They are working on surgical procedures to replace the cartilage, either with lab produced cartilage, or by growing new cartilage from a sample taken from the knee. Unfortunatly they are not very successful yet.