Kridda, I've determined that my washer sucks. I think it was the cheapest front loading washer available at the time. Another issue I have is that we have VERY hard water. I was using vinegar and then started reading A LOT of stuff about how you are NEVER supposed to use vinegar on your diapers if you have hard water. I'd be afraid the combo of vinegar and baking soda, even if not at the same time, would cause a foaming reaction and huge mess due to residue of the baking soda left behind. I have to handwash all of my poopy diapers because my machine wont get them out at all, and it's EBF poo too, so I wouldn't trust my washer to get the baking soda out. It's been a delicate journey trying to figure out what works.
Jackie, it's random and doesn't happen every time or with just one type of diaper. My first thought was that it was too tight, but it was already on the biggest setting, and when I stick my finger in there it's really not at all tight.
Erin, I'm scared to put bleach on my covers and pockets. I've ready you aren't supposed to do that because it breaks down the PUL. I'm also concerned that Kole has sensitive skin and would react to the bleach if I didn't get it all rinsed out. I may still try it with a few though, if I can't figure out another method.
Bleach will cause the diapers to break down a little faster than they would without bleach but its worth it in my opinion to get rid of ammonia burns and stink. I add a half cup to my hot wash and then give it a cold wash after that instead of just an extra cold rinse. I only bleach about every third wash or so, which is maybe once per month now that T's day trained. I say give it go. You'll want to use half as much with your front loader as I use. You can even start with less than that to make sure Kole's OK with it. Stick your sniffer in there after the wash and give a few extra rinses to make sure the bleach smell is gone.
I've boiled when I had one offending diaper that I got second-hand and that worked to get the ammonia out. Then I got the brainy idea to boil all my diapers, but that never actually happened once I realized I could only reasonably fit 3-4 dipes at a time in the pot that I have. I really didn't want to be boiling diapers all day. I have used bleach too, but I wash my diapers as usual first, take the covers out and hang them to dry and then use bleach only on the inserts and prefolds. I have also used oxyclean (I bought the kind with no additives). Let the washing machine fill up with hot water and let them soak in the oxyclean for 15 minutes or so, then turn the washer back on and wash as normal. All these methods seem to help when I start to get a little bit of stink. I can't complain though. I haven't had too many issues. I think it might also help that I have only ever used one kind of detergent. It works, so I stick with it.
Maybe try an oxyclean soak overnight first. I did do that soon after moving here to help get the funky issues out of my diapers from my RnG HR issues last winter. Fill a tub or something big with HOT water, add a huge scoop of oxyclean (look a likes are fine), mix, then add diapers. Mix again. Leave it.
Since it's just the pocket covers I'd do this to first you should be able to hand rinse them easily enough. Just do 1 or 2 at a time since I know your two kids don't give you much peace. ;)