I had these same kinds of growth anomalies in my tank for the last year. Corals just encrusting and getting really thick with no upward growth. Deformed looking polyps. Hyperplasia on the tissue.
Seemed to affect some corals quite severely. Others seemed completely resistant to it (all my Tenius, though they still didn't grow much). I read all the different threads I could find on various message boards about this, but the consensus seems to be that no really one knows the cause or the cure.
That said... in the last month my tank seems to be starting to recover from this issue. The main thing I changed was that I realized my Alk levels were significantly lower than what my Alkatronic was reporting. It said it was in the low 8's, but in reality it was in the low 7's. I corrected the levels, and have monitored all my major params and kept them as stable as I can. Within a few weeks of doing this, 4 different sps frags that hadn't done anything but encrust for the last year suddenly started sprouting new growth tips! A few of the frags that had severe hyperplasia (ie: the "bounce" bubbles on the tissue) started to "heal" and the bubbles have slowly been going away. Along with that, I started seeing polyps coming out on corals that had zero polyp extension the past year. Some of the deformed "tulip" looking polyps have started to regain the normal shape/color.
No idea if it's ACTUALLY related to Alk levels? But that was the last thing I changed on my tank that seemed to make a difference.