If those are Plumbing pipes you are talking about then when water runs through them they expan and rub againt the joist, but it sounds like you have a stoppage in the pipes are a bad job of plumbing, and venting. It is kind of hard to fix if you cant see the job. Some times when they go through the walls are floors they cut two small of hole and pipe expans and makes a noise, but way you say it does it all night, so you must have a toilet are some fix. leaking. check the toilet flapper in tank, call a Plumber if you cant fix it.