ok guys i talked to a guy from specrapure and this is his response
John,
The DI stage would be the the most likely cause of ammonia in the permeate water . Most DI cartridges are good for 300 to 600 gallons with chlorine in the tap water. If there is chloramines in the tap water the life of a single stage DI (after the RO) will be rather short. We always recommend at least two DI stages if there is chloramines in the tap water.
In addition the carbon filter may be depleted. Check the brine water for free chlorine. If there is chlorine in the brine water the carbon filter should also be replaced.
Izzy also told me he had ammonia in his ro water as well. I have read that low water pressure can cause a membrane to prematuraly break down. They sell pumps to up the water pressure going into ro unit but I did not see what level of pressure would cause this or do I know how to test pressure going into my unit. Thought that this might be a possible cause.If anyone can come up with something else please let me know. Thanks. Tarvis let us know if yours test for anything. Anyone else that would not mind to do so check yours as well and lets see what we come up with.