I've had this problem on and off for years now and it's almost always an alignment issue with tops and bottoms of walls. When reverting to default tops and bottoms (when I want them at the default) doesn't work, "updating" the plot line view a few times in layout would usually fix it. Today though, had it happen between a main level wall and an attic wall (gable wall above main level wall) and NOTHING would work. I redrew whole walls, quadruple checked alignment, everything...
I finally just switched the main level wall to balloon framed and that fixed it. Just wanted to add this workaround to this thread in case someone has a similar issue and it pops up in a google search like it did for me.
I'll acknowledge that if you do the whole build framing thing (I don't, only provide arch plans) this may not be a solution for you.