Is your water disinfected with chloramines? This is the likely source of the positive and harmful ammonia readings. If so, you should be using a neutralizer such as Amquel or Prime to break the chlorine-ammonia bond, neutralize the chlorine and complex the ammonia.
Ammonia and ammonium are different from each other. I'm not going to go into a detailed explanation but the difference is caused by ph somewhere around 6.5 I do know r/o's do not remove ammonia. So like RTR said it's time to use Prime or Amquel. I use Prime with my r/o water because I have chloramines. If you read the bottle it says to use at half strength with low levels. So I use 1 ml per 20 to 25 gallons. You have low levels do to the fact your r/o prefilters have removed the chlorine.