Reaching a bit here, not sure what is going on. It almost sounds as if you have it set up to keep copies of configs whether or not if they've changed or not. That is assuming your "Comparison Criteria" rules are working. I found something that might matter, but not sure as I've never used it.
Under "Settings" / "NCM Settings" / "Real Time Change Detection" / "Config Downloads & Notifications", do you have it set to "Last downloaded config file" or "Baseline config file". If set to Baseline, change it to Last Downloaded....