Yes mine does that as well, and I have also seen my green cyano go transparent during the dark phase. They are adjusting pigments somehow, not moving their structure.
By the way, if you have red slime mat on your sand I want to recommend a product from a personal perspective, not a RDO persepective. The product is called Boyd's Chemi-Clean and it will zap the red cyano gone in three days. I used it in my nano aquariums and it fixed my problem perfectly, if it didn't work I was going to tear down my tank and start over. This product is extremely potent, and you can damage your corals by using too much. If you use the directed amounts, it works wonders is all I can say.
I have never been a proponent of using non-natural meds in a reef system--usually careful consideration of biological and physical components is all that is needed to build a reef that will run indefinately. But, somewhere along the way one can mess up and in my case it was a heat spike that killed off much of my microfauna. After that I feel the tank started to rot, giving this cyano a foothold on the extra system nutrient.
Boyd's was a great 'cheat' that helped my system get back in line after the bungle, I will always keep some on hand from here on out. The product says it does not harm marine inverts, macros, pods and bacteria. Apparently it is a strong oxidizing compound that 'burns' the bad algae in a couple days.
HTH
B
