The main reason I don't use the type of filter you are describing is because every time you put in a new filter pad, the tank basically goes through a whole new cycle again. By throwing away the filter pad you are throwing away the bacteria on it needed to convert ammonia to nitrite to nitrate. In my opinion that's the main problem you are having, unless of course your tank has a bio-wheel. Your substrate and any ornaments you have will have some bacteria on it as well, but in my experiences not enough to prevent another cycle. Is it possible to maybe change the type of filter you are using? Maybe something like a mini aquaclear? I think it would help. Just my opinions...
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