Clownfish are jerks. Let me repeat that: clownfish and anemones are *jerks*! There, I feel better anyways. :)
I hear you about ammonia in an established aquarium, and yet here we are trying to guess what the cause is. I was surprised to see my 125 gallon, multi year old tank with many fish in it test ever so slightly positive at one point (I think because of a missing/dead fish......or did that fish go missing because the ammonia was already there?). True, one would expect that most fish would be afflicted by similar poisoning, but you have been in the hobby long enough to know that not all *will* be affected by everything equally. So my advice is check off the easy to take care of things first before worrying about more esoteric causes. *jumps* off my soapbox. Glad to hear he/she is doing better in any event!