The situation above is why I recommend any system with ammonia permits run both ammonia and TKN on the influent. To understand my reasoning, let's look at the tests.
First, ammonia testing is run by one of several methods. A common method is to use an ion selective electrode (ISE) to measure ammonia gas from a water sample to which sodium hydroxide is added to facilitate the conversion of water soluble ammonium (NH4+) into ammonia gas (NH3). This and other EPA approved methods, read only the ammonia/ammonium portion of total nitrogen in the water.
Now the TKN, also called Total Kjeldahl Nitrogen - after Mr. Kjeldahl the inventor. This test has more steps than the ammonia procedure as it relies on an acid digestion step that converts organic nitrogen into ammonia. Organic nitrogen includes proteins, amino acids, amines and other nitrogenous compounds that during biological treatment will tend to produce ammonium/ammonia. After digestion, the amount of ammonia is measured. Therefore, for any sample: TKN > Ammonia. TON or Total Organic Nitrogen is simply: TKN - Ammonia = TON
For the wastewater system mentioned in the first part of this post, the influent TKN was significantly greater than influent ammonia. Alkalinity and aeration while sufficient for influent ammonia was insufficient for the ammonia derived from influent TKN.