Also you may want to try tweaking your layer settings to change your layer priorities. Where a wall intersects with another that is not cleaning up correct, place them on separate layers and assign a different priority like a 3 to the problem wall. This will make it so the don't try to clean up at all. You can then fake a wall clean up by turning the corner as suggested below, just enough to appear as if it is cleaning up. You can always use a SEO to hide odd intersections that poke through.
Try wrapping each complex profile 1 mm back at right angles to finish the wall end
AND
adjust wall priorities to make one wall clearly dominate the other
Your walls most likely will not clean up if you do not have simular reference lines, composite fills, or priorities.
Your wall that is disappearing is prob because you are intersecting with a wall either above or below it. Priorities can help here too, or adjust your heights.