My first guess is that the complex profile wall may be interacting with another wall or beam element. I think a floor plan view with Wall & Beam Reference lines turned on and surrounding walls pointed out would shed some light on this. Also a shot of the complex profile in the Profile Editor drafting pane to cross-reference with the floor plan view would help as well.
But for something to try you may just want to select the walls with the intersection problem and for testing purposes place them on a separate layer. Then change the Intersection group number to a number that is unique from the rest of the layers. (the little numeral in the Layer Settings dialog to the left of the layer name).
Best regards,