That slicing is caused by data errors during capture, not as!3. Because it causes sharp lines the analysis thinks these are the best frames and puts them at the top of the pile. This will cause a very poor stack.
Simple to fix. Scroll through the frames after analysis and when you see a corrupted frame press the space bar to tell as!3 to ignore that frame. Redo the analysis and they are gone. An make sure you use a good frame when adding align points. Problem solved (hopefully)!