Why does water suddenly stop running then start again after a couple minutes?

If you get a clunky knocking noise from the pipes of your water system it is air-lock, like an air bubble in the pipes. The only way to get rid of it is to let the water run or if you have bleed-points bleed it (put an old towel down first) It is common for this to happen if you have turned the water off or drained the system for maintainance.