Continuity mistake: Martin covers the girl with a blanket in the "evening" while the boy is chasing the fireflies. It is never cool enough in GA during the season of fireflies to warrant a blanket. Never. Unless there was some weird and unexplained weather phenomenon. (00:56:00)
Revealing mistake: Near the end of the movie, when Malcolm's partner pulls out his gun and Lester shoots him, the bullet hole in the wall appears before the bullet wound in Paul Giamatti's arm.
Answer: The "draining noises" are Big Momma taking a dump. Big Momma didn't flush either so I'm assuming he took a look at her stools and what he saw made him feel sick.