So sorry to be the bearer of bad news, but yes that's what is causing your issues. The scent in the ammonia is like poison to bacteria, unfortunately.
Depending on how much money you have in the tank right now in terms of gravel/substrate, decor, you'll have to make the decision to try to clean everything, or just toss it and start anew.
If you want to clean it, drain the tank and take everything out and just rinse, rinse, rinse, rinse, rinse. After you've done that, rinse it some more. The tank you'll need to clean as well using lots of water and maybe a 1:20 ratio of white vinegar - then rinse it out a LOT.
Filters, heaters, gravel, fake plants, sunken ships, skulls, treasure chests - whatever you have in your tank will need to be rinsed extensively if you want to save it.
Any filter media you had in there just throw it away - it's virtually impossible to get sponges, carbon, or bio-media clean because of how porous it is.
Then, unfortunately, you have to start your cycle all over again. If you have a friend that can supply you filter media, gravel, or anything from their tank that's loaded/seeded with bacteria, that will definately make things go faster this time around. You can also ask your LFS for seed material too - they look at you funny, but usually comply.
If I didn't mention it, you gotta rinse everything really really well.
I keep saying it, and I'm not trying to be funny or antagonizing, I promise - I'm just trying to iterate how important it is to get all that stuff really clean so you don't have this problem again.
Ace Hardware is the only place I've been able to find pure ammonia. They call it "Janitorial Strength" and nowhere else I've looked has trully "pure" ammonia.
Depending on how seeded the filter media is, your cycle can be done is as little as 7-14 days. I don't want to get your hopes up, as this is rare, but it is doable. The more stuff you can get from your friend the better - even if you don't keep it in your tank after the cycle is complete. Fake plants, gravel, anything you can get will help - although filter sponges are the best.