Andy, I had an episode like that about 4 months ago that came to a head. I was fighting it for over 8 months. Along with the recession I also noticed when fragging that the freshly clipped corals would not encrust. (even after 2 months) I decided to do a reboot & prior to doing so took a large portion of my corals out of the tank & housed them with other reef friends. (thanks Lam, Ed, Jeremy) I decided before doing the reboot I would send my water out to a lab for analysis. (I thought I may have traces of copper, lead or zinc present in the tank. After 500.00 plus dollars in testing it was evident. I had extremely high organic levels in my tank. No Po4, No nitrates or Ammonia. (even down to as low as ppb...that is except for po4, very slight traces at that level) The thing that was strange was....I had no nusience algae whatsoever. (I mean it!!!) A reef tank should not have an organic level higer than 1.2 ppm. (that is unless you have a "sewer reef" without any SPS present.) Well my organic level in my tank was at 3.4 ppm. I feel now that the cause was multiple water changes w/ NSW while doing the 3 phase interceptor treatment last summer. Though I believe NSW is better than synthetic salt in alot of ways.......The water we collect is high in phosphates & organics. (at a lab grade test that is) Not from the tests sold over the counter for the reefer. Plus you must take into account the microscopic life forms in local NSW. They are adapted & native to cooler water temps. When you introduce them into a reef tank with higher temps they die off which raises the organic level.
Something to ponder......
I've since stopped the collection & use of NSW & I have noticed a marked improvment. Not only by me but by the guys who helped house my corals for a bit while I was trying to obtain a solution.