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What kind of filter are you using, make and modle? I know you said no ammo in water, and chlorine or chloriamine are threats, but have you tested the nitrates and nitrites? This may be the issue. When you tranfered your filter media, was it allowed to go without water / air flow for more than 30 min? If high levels of bacteria are in the media and it doesn't get oxygen then that could cause issues. When bacteria die in mass they leave behind some nasty substances.
 
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