I've been wrestling with the same problem for over two months. All of the zoas in my mixed reef are closing for large portions of the day and when they do open their skirts aren't fully extending. Yet, they do seem to be splitting regularly.
I'm really stumped on this, so I'll be following along with this thread. I'll share some of my systems attributes in case we can identify a similarity.
My params are:
Sg 1.026
Temp 78
PH 8.2
Alk 10dkh
Ca 425
NO3 none register
PO4 0.03
Turnover in display is about 45x
6x54 T5 w 4 actinic blues, 1 actinic white, and 1 fiji pink. The 2 oldest bulbs are 9 mos, the rest are 1 and 5 mos.
I did recently kill the lights for 48 hrs to kill off some cyano on the sand bed and did notice that the zoas perked up a lot.
I've tried feeding more, and running less carbon. That seems to have helped a little.
Lighting was suggested as a problem, but my SPS are growing like crazy, so it isn't too little light. I also have a lot of shaded areas, but the zoas in those places react the same way as those in high light areas. Same with high and low flow areas.
I was adding two part by pouring it all in one time daily. I am adding 100ml of Alk and 70ml of Ca. I just switched to dosing pumps that run 10x/day 30 minutes apart to avoid swings. I'm also going to reduce the Alk to 9dkh.
I also haven't observed any predators in the tank, or any fish picking at zoas.