Why don't you just ask HIM?

Anyway, I always thought that meant a flush to cover up the sound ??

So I don't know what he means. Hence why you should ask him to get the 'correct' answer. One idea is that he wants to know when you're done, so he can get in. A flush would alert him to when the bathroom is essentially free.. should he need it.

I guess since all the other answers are talking about a smell, I might be wrong. But flushing quickly doesn't get rid of a smell, and frankly why would someone announce via a premature flush, that they have just depositied something especially stinky ? Yuck. Plus you would need to be hanging around with your pants down if you got rid of it so quickly. Doesn't make any sense.