Could be something rotting deep in your gravel or it could be your ammonia detoxifier messing with your results. Do you dechlorinate your fresh water before you add it to the tank or after ?
I've had no fish or anything go missing since I relayed the gravel in the tank so I can't think of anything that could possibly be rotting away and yes I was leaving the water out for a few days before adding it but now I use API stress coat to dechlorinate it. Also I'm going to get some Seachem Prime as soon as I can get to a shop that sells it
I'm inclined to think that your gravel probably isn't as clean as you think it might be, especially as your pH has suddenly dropped. That indicates an overload of organic matter somewhere in the tank. So you need to really go to work on the gravel (right down to the base) and clean any muck off ornaments and plants. Then you need to raise your pH to help the bacteria as they are not very efficient at pH 6.5 (and that will probably continue to drop). If you tap water is at a higher pH (it should be because you said your pH was 7.6 before) then change about 30% water every day and that will help to stabilise the pH at a higher level until the filter gets going properly.
Do you have good aeration in the tank, either by ensuring the filter outlet is agitating the water surface and/or by using a bubble stone?
