This is likely too recent, and there are other phenomena throughout the house. But, I'll give it a try:
"The Messengers" (2007)
It's been six years since the Rollins family left their farm, and now the troubled Solomon family has come from Chicago to rebuild their lives following their son's hospitalization due to their daughter's drunk driving accident. As they start to settle in, something odd and strange begins to occur to their son. Could something supernatural be at work, and did the previous family just leave, or are they still here?
The persistent stain is on the parents' bedroom wall as far as I recall. Even when it's painted over, it shows up again. Shadowy figures keep showing up, sometimes violently.
At least it's another film to rule out.