First of all, i would agree that you should get another test kit and try for a third opinion on your NH3. Have you taken a water sample to a LFS to see what they read?
Were your tanks brand new or did you buy them used? What about your other equipment ?
I am assuming you have no livestock at the moment?
If you truly do have NH3 and if I had to guess (which I totally am btw), I would guess that something is occasionally killing off your nitrifying bacteria. There are a host of things that you unbalance your tank causing bacteria to die off. Nitrifying bacteria can die of Chloramines or Chlorine, temperature, fresh water, lack of oxygen, ect, ect...
Have you been performing water changes at all?
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