So someone suggested that my last post maybe needed a little clarification. Three to four elements have been found to be key in successfully keeping a reef aquarium. The first is a mature, well established tank; some corals, particularly softies are very hardy and will ok in a tank that is not fully matured or stable, others will not. Second is chemical composition (including salinity); in many ways this goes hand in hand with maturity - when levels like salinity are not stable and where they need to be, it also usually means that other elements are not where they need to be, as your salt is what sets those levels in a reef tank. Third is proper lighting; you are already making some adjustments in your lighting so that is good. Fourth and often described as most important, is water flow. Water flow on a natural reef system is amazing - these animals cannot move, so they rely on water flow to eliminate waste and bring in new fresh water. Without currents, they would drown in their own muck. Flow in the reef tank is no less important, therefore a scape is not only about creating a spot to provide placement for coral, it is also about being shaped and open enough to allow the maximum amount of water flow throughout the reef area as well as provide for water movement around your coral placements.
My observation was that your initial scape did a much better job of meeting those goals than your current scape does, therefore it may be to your benefit to look at revising your scape in an effort to meet those goals, if maintaining a high quality, functioning reef system is your overall goal.
I used to know where the two very well written articles on water flow were located, but I lost my bookmarks when I changed search engines, so I'll have to do a little looking to see if I can refind them for you.
Hopefully that helps clarify some things.