We had this problem a few months back. It was really annoying especdially at night. As soon as the loo was flushed there was this loud noise vibrating from somewhere and as we live in a bungalow, it seemed to vibrate through everyroom!!
Eventually the answer was found. It was a small valve on the toilet (something to do with the where the water enters the cistern)The valve was easily adjustable and after a tweak or so-no more noise. Its been fine ever since.

Hope this helps,
Lauraine.