sounds like it could be a faulty ammonia test with your kit. you can get the different tests separately (i know petsmart carries the individuals for API). i'd get another ammonia test and report back to us what your readings are on it.
when i clean my test tubes, i run them under hot tapwater, as hot as my hands can stand (which is pretty darn hot), tube in one hand, cap in the other. i fill then dump, fill then dump the tube, then fill it halfway and put my finger over it and give it a good shake, do this again, then fill and dump two more times at the minimum. with my other hand, i keep the cap under running water the whole time i'm rinsing the tube. then i lay the tubes and lids on a paper towel to air dry. never had a false reading with my kit by doing this cleaning method.