If I were a betting man I would put my money on an intermittent stray voltage or shock. I remember my uncle talking about a few stray volts causing cows to produce less milk. Now if a "few stray volts" will affect a cow like that, what would it do to a fish? Maybe your system has progressively been putting more current or voltage into the system over the last couple of months. If so, this is why your established corals and fish aren't bothered by it. I remember reading about people using electric current in accelerating reef growth in some of the areas devastated by the tsunami waves of Dec 2004. Anyway, I digressed, if I were in your shoes I would seriously look at properly grounding the system for 2 reasons: 1) it hopefully will solve the problem, and 2) it can't hurt and will probably help the overall health of the tank.

just my two cents.