Here is my current best guess, based on what I have so far heard about your situation.
I have actually ran into a similar problem not to say that your is the same but it might be a place to start looking. I will try and explain the cause that I found and what we did to fix it.
A friend of mine had a town house and we would here a creeking/knocking noise in the wall going up o the second floor whenever hot water was used in the upper floor. This noise would last about 2-3 min after the water was started to be used. then it would stop even if hot water was used again. Wait quite a while and again it would do it when hot water was used.
What I found was the copper hot water feed for upstairs was strapped firmly to the 2x4's of the wall. When the hot water caused the pipe to expand it would creek against the wood as it was forced by the clamps. We had to open up the wall to find this but if it is a crawl or basement were the noise is it should be easier. We ended up using a different kind of strap made of a hard plastic and a thin piece of plastic between the wood when re-clamping it. This allowed the pipe to silently expand.
Like I said this may or may NOT be your problem but it is worth looking in to.:confused: