Perhaps it is because of bone demineralization which is not osteoporosis but osteomalacia. Here a doctor explains:
Demineralization means that the bone has an abnormally low amount of mineral in it, especially calcium and phosphate.
The mineralization of bone is an important part of bone strength. Osteomalacia (softening of bone) is a disease in which demineralization leads to an increased risk of fracture. When this affects the bones of growing children, it’s called Rickets.
Osteomalacia is different from osteoporosis. Both can increase the risk of fracture. But osteomalacia is a low mineral content in bone. With osteoporosis, the bone is more “porous” and has a reduced mass.
The most common causes of osteomalacia include:
Not enough vitamin D — Vitamin D can be low due to a diet that does not have enough vitamin D or by not getting enough sunlight (less than 10 or 15 minutes daily).
Liver or kidney disease — The body may not be able to regulate vitamin D the way it needs to when these organs are not working properly.
Celiac disease — This is an immune reaction to gluten (a protein in wheat and other grains). It damages the small intestine and can impair how vitamin D is absorbed.
Cancer — Certain tumors can disrupt normal mineral metabolism.
Surgery — The stomach and small intestine play a part in absorbing vitamin D. Surgery that removes or bypasses these parts can lead to low vitamin D levels.
Medications — Drugs taken for seizures, such as phenytoin and Phenobarbital
http://healthyliving.msn.com/diseases/osteoporosis/bone-demineralization-1
The last part is interesting as I only noticed my bones clicking when I began taking the Gabapentin (traditionally used for epilepsy) to restore my deep sleep stages.