It could be that the substrate holds a great deal of BB.
After thinking about it, in regards to my situation, where something similar happened, my opinion is that it was the loss of the biofilm, and bb from sand/substrate, causing a poor environment. I know I did water changes less frequently and maintained the same schedule, although I had less bb to process everything the same as before the tank change. I didn't take into consideration that little info. and I wasn't testing the water because I had been on auto pilot so long, I didn't "need" to.
Also I would check your kh/gh and tds.
Sometimes it is a molting problem. Not enough nutrients and or calcium.