Sounds to me as though your water has extremely low buffering capability. The crushed coral you'd been adding to the filter was maintaining that buffering capacity, but without it... the water does it's 'natural' thing which is the formation of nitric acid (nitrate) as the end result of the nitrogen cycle. When that nitric acid builds up, it slowly erodes whatever buffering capacity is in your water quickly causing a pH crash. (More nitric acid is produced all the time and once the buffering capacity of the water is reached the pH starts dropping.)
I don't think that anything is 'wrong'. That's just your water chemistry. The phosphate remover might be removing some of the buffering ability as well. Personally, I'd just keep adding the crushed coral as you have been... and make sure to ever remove it for an extended period of time. Oh... and be sure to replace it as necessary.
As for the fry tank... I'd add a smaller amount of crushed coral to that, so that the water parameters in the two tanks are as close as possible.
I don't think that anything is 'wrong'. That's just your water chemistry. The phosphate remover might be removing some of the buffering ability as well. Personally, I'd just keep adding the crushed coral as you have been... and make sure to ever remove it for an extended period of time. Oh... and be sure to replace it as necessary.
As for the fry tank... I'd add a smaller amount of crushed coral to that, so that the water parameters in the two tanks are as close as possible.