I have read the entire thread (2 pages for me lol), and can still not make heads nor tails of what the OP is doing. Might I remind you the OP is not even certain what his tap water is treated with, let alone what the residual is at his tap, so that may in itself be an issue depending on the chlorine/chloramine residual at his taps. So, for me personally, newb status applies. 6 months in or not, very easy to screw things up if you don't understand the science behind some of this. BTW - I have never had an issue with Prime or Safe having a negative affect on a cycle, nor is there any reasonable explanation as to why it would. Ammonia binding products simply convert NH3, free ammonia, to a fish safe form. The ammonia is still available to the bio bacteria. Not sure what happened to you in the past, anymore than what is going on here, but rather certain that it has nothing to do with the OP using Prime, unless he wasn't using enough? Who knows, I hate playing guessing games.
Good luck figuring it out.