You are right by saying that exercise helps you in many ways and if you stop it for a while, you will find changes.
To build bone mass, you need to do some weight bearing exercises, in the form of walking/jogging and weight training. You should ensure that your routine contains equal exercises for ALL parts of the body. By equal, I mean, what you do for the back of the body, should be done for the front, what is done for the top, should be done for the lower half. This will ensure there is no IMBALANCE in your body and at the same time, may help in building your bones stronger. Even though you find that muscle fibres are growing, there is no doubt that your bone mass also increases, if you do the right kind of exercise and do it in the correct manner. You might also like to see an orthopaedic specialist.