Please Help Pond Fish Dieing

I have two large ponds, One pond is higher than the other (only
slightly) and runs into the other pond. There is then a pump that
takes the water through a filter then back to the top pond. My water
have been tested for Amonia, Nitrate and Nitite, and all read zero.
The strange problem is the fish is the bottom pond have started to
Die. They stop eating, stay at the bottom of the pond them come to
the top to dye, twitching and listing as they go. They look very
healthy apart from clamped fins. There are no visible parasites like
flukes or Ich. This is not the first time it has happened. last time
I think I stemmed it by adding salt or it may just be
coincedence(parasite / bacteria medications have no effect) it went
away so I restocked and now 5 months down the line I'm here again.
any ideas ? remember the top pond is never effected ?

MIKE