Hi, I used cloth diapers for only a short time, but I want to try to clarify your question a little bit. I was wondering what "that smell" is. Is it ammonia as someone else noted? If it is, there won't be any reason to read further. I wanted to touch on something that hadn't been noted.
The first thing that came to my mind was a mildew smell. We have this problem with washcloths that we clean the kids up with after eating. The cloths would seem clean until we dampened them and we would experience a "smell." I thought with diapers also being damp, this could happen too. We would bleach on occasion and that would remove the smell for a few weeks. I really don't bleach, as I don't like the smell. Now we have a new washer with a sanitize setting. This has worked wonderfully. Now I know this is a new sort of option on machines, but the hot water treatment might work. You might have to do this in your sink or tub and add boiling water to the hot tap water. Tap water alone does not seem to get hot enough. I wish I had a time and temp to offer. If it is in fact mildew that you are experiencing, maybe someone else knows the details if done by hand.