Hi A.,
I am not sure what you are using for stuffing in your pockets, but I have found that cotton is the easiest to keep clean and free of ammonia smells in the high efficiency washers. If you just notice it occasionally, they you probably just need to wash you diapers once with out soap, then use more water and less soap or have more rinsing in the future.
If it is something that keeps coming back they you probably have residue in your diapers. You can strip them by washing them by hand with blue dawn dish soap...just make sure to rinse fully, this should take care of the problem. You may also want to try a different detergent that leaves no residue. We have tried many different types but have been very happy with Charlies Soap for about year now. The only thing with Charlies Soap is that you have to use it for all your laundry and should never use softeners in the wash or dryer. You can use Baby Oxy Clean with it to sanitize, and distilled vinegar for a softener.
Best of Luck, it is great to know that there are more cloth diaper users out there!!!