I haven't even begun cloth diapering yet, as my baby girl isn't due until next month, but I was just reading on the Ragababe website and came across this. Perhaps it's your problem?

"If you notice an unusually strong ammonia smell on the diaper after your baby wets, it is usually because the ph level has become too alkaline. This can also lead to rashes and cause your diapers to repel liquid. The number one cause of this is detergent residue build-up, which may be the result of improper detergents or using too much detergent. It is also possible, if using a front loading HE washer, that too little water is present. (See HE washer instructions above to increase the water level.)If this is a continual problem, you may have to strip your diapers (see Striping sectionbelow), to get a fresh start -- and try these corrective actions. As mentioned earlier, spraying BacOut onto diapers and inserts (especially if worn all night), will help reduce the ph level because of the acidity of the lime. You can pour BacOut directly into the cold wash cycle, but treating individual diapers before dropping them into the laundry bag is more effective and helps keep any smell at bay until laundry day. If you notice an ammonia smell on diapers coming immediately out of the wash, you may not be using enough detergent, as the urine is not being removed sufficiently -- or again, waterlevel could be too low."