If you ever run into a situation where a surface, running across multiple elements, looks correct in 3d, but is misaligned in elevation, the problem may be due to the wall or beams direction. We ran into this recently on a project that, despite all the efforts to align surfaces in 3d, change surface settings, surface fill settings, or even redo portions of the model, the surfaces did not clean up correctly in elevation.
Fig. 1.0 Misaligned Walls In Elevation
This was a difficult one to duplicate, since the align surface command works for most surfaces and conditions. But in this particular case the wall was a bit of a jig saw puzzle and alignment was always slightly off. The issue was the walls orientation, or direction, and not the surface settings. Ideally walls should be drawn in the same direction when they abut. To check the direction of the reference line of a placed wall go to View > On-Screen View Options > Walls & Beams Reference Lines. This will show the location and orientation of the wall or beam in a floor plan view.
Fig. 1.1 Wall Reference Lines Direction/Orientation In Plan
This is not something I recommend checking for, but rather keep it in the back of your mind for when you find a tricky elevation that does not seem to align properly despite all the align surface attempts. The fix is to simply mirror the wall from its center point perpendicular to the reference line in order to get the correct or matching direction of the walls below or adjacent to it.