Hey Sparks,
could you give a little bit different view of your problem roof? I can't tell where the roof is coming thru, what's the front door wall? floor plan shows a door, but the 3d view seems to have a window there. I am having a very similar issue, gutter inside the house. I tried Join roof planes on mine, but to avail.
Also, could you show where the breaks were placed? Yellow is the whole roof plane, the red part is what wraps around and goes inside the room.