I have been having some of the same type of problems with my BB system. I have had two corals completely fade-out and I have had a little STN and decrease PE on two others. My macro algae is not growing well in my refugium. But I have been unsure of the cause. I have been traveling a lot which is never good news for my tanks because things do not get fed they way they should. I also had my co2 regulator break and I ended up with some big flucutations in my CA and Alk level until I replaced it. (It took me a while to realize that I could not get it to work) I can be a slow learner sometimes :>)
In the meatime, other things are doing great! Old standby SPS are going and showing great color and growth. The anemones. clams, leathers and LPS are all growing.
I started the new 300 gallon set-up in November. I did cook about 90% of my old rocks for about 6 weeks plus I added about 300 lbs of new LR that I cured.
I do weekly water changes of 10% and I change filter socks twice a week.
I was thinking of adding sand back into the refugium anyway and I am going to buy some uncured LR, cure it, and add it to the refugium. I prefer the look of sand in the tank but I hate the idea of adding sand to the display due to the increased risk of scatches. I will step up my feeding the next few weeks and see what happens.
I wish I had answers, I just thought I would add my problems to your excellent thread and keep reading.
Thanks,
Connie