It's been my experience that tanks using Ammo lock get a so called "false positive" even after a 100% water change (after a day or two anyway). So unless it works 100% effectively in trace quantities (which I doubt) people are actually reading Ammonium from some other condition. That's the other thing, in low pH NH3 picks up the free hydrogen and becomes NH4.
So far as the prime, what type of test did you do? NH3 or NH3/NH4? It should be in your directions and/or on the bottles somewhere. If one tests for NH3 while using a chemical you should only get trace/no reading. If it's a NH3/NH4 test then you should always get some reading, regardless of chemicals, if either are present. When you get down to it, Prime can't just make it "go away" otherwise you would never cycle the tank. The nitrite and nitrate are going to be detoxified in a completely different manner, not sure what that is though.
Either way, I use Prime too, have for YEARS and the only way I'll stop is if Seachem stops making it (knock on wood that they don't).
Chris