The walls that are not joining are on a different level to the walls that join ok ?
I have found that sometimes this happens due to behaviour of walls on a level below or above. Perhaps the walls from the lower level extend above the floor level and are overlapping or the wall cladding could have a top extension or bottom extension that could be extending into the problem wall ?
Another one I have found is if wall elevations have been edited in profile.
Hope this helps.
