If you aren't using salt (what I prefer) to treat ich, malachite green + formalin (rid ich, and quick cure) are a great combination. When used as directed, does not harm beneficial bacteria, but if you over dose, it can crash your cycle.
Glad to hear your water is still ok
But what caused the ich in the first place? I've found water quality to be the #1 source of ich infestations. Are you testing your nitrAtes correctly? You may already know this, but you have to vigorously shake bottle #2 for at least 30 seconds before adding them to the water + bottle #1 solution (which also has to be thoroughly mixed before adding the drops.) Also, you have to shake the final concoction for at least 60 seconds, and let it sit for 5 minutes before reading results.
Even with routine water changes, nitrAtes can climb to incredibly high levels and cause stress on fish, and if your ammonia/nitrIte aren't the problem, then my first suspicion would be nitrAtes.