Hi Peter,
The problem with the odd angles in the roof is that probably you have not set the angled edges to Gable. When you draw a wall 'By Picking Points' it does not have to have a wall to sit on, so no need for invisible or even mini walls. The mini walls are only needed to create rooms or gable end fills withn the roof area, so they will accept doors etc.
Walls automatically extend to the roof by default. If there is no roof on that location, then they will extend to the wall height specified for that Location. This appears to be what is happening here. Either that or you have the second locations 'floor level' at the same height as the wall height of the first and have not allowed for the thickness of the first location's floor, as the extension appears to be about the standard 305mm floor thickness.
I will try that again(!): Ground floor floor thickness is 300mm, wall is 2400, so second floor floor surface is 2700 above the terrain (0). If you have the roof on another location but did not allow for the floor thickness also, it would be 300mm lower.
If the roof is at the level you want it, then just reduce the height of the walls that stick through.
If that does not solve the problem them post or email the BLD file as it is much easier to diagnose that way.
Allan