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Visit Fluff Love University http://www.fluffloveuniversity.com/, and join their facebook group Fluff Love & Cloth Diaper Science. They will get you straightened out.

I can see a few problems you probably have:
1) Charlies Soap is not a recommended detergent
2) Are you doing two full washes? Your diapers are probably not getting clean.
3) Do you know your water hardness? By adding borax you may be over-softening your water which causes problems getting all the gunk out.

Don't throw in the towel, they will be able to help you!

I agree with Fluff Love.

My microfiber inserts stunk awful and I followed their instructions for stripping and they haven't smelled at all since. I used Grovia Mighty Bubbles and bleach.
I use regular Tide now with no Borax because we are on city water and it is already soft. With Tide the water can be harder before you need to add Borax so you might be over softening. Each load gets washed twice with detergent. And if your water is actually hard, you need to make sure not to do an extra rinse.
I have heard really bad things about Charlie's Soap too so you might want to stop using it.

We ended up switching to Ecos Free and Clear as our diaper (and main) detergent and didn't have to deal with barnyard stench a lot. I mean, yes, sometimes you get there and need to strip, but it wasn't regular. I used a local to me stripper available at a cloth diaper store, but I would check out fluff love and try their routine.

In regards to water hardness, you can use pool test strips to figure it out:
http://www.fluffloveuniversity.com/how-to-wash-cloth-diapers/dealing-with-hard-water-and-cloth-diapers/youve-done-a-water-hardness-test-now-what/

or use this poll:
http://www.fluffloveuniversity.com/original-experiments/participate-survey-time/water-hardness-by-area/

In regards to stripping, MF stink, fluff love, etc....
I stripped all used diapers before LO came. All of our system is MF pockets or AIOs. We've been CDing for 22 months consistently, one kid only though. No stink or stains or any issues at all using Fluff Love's routine.

We use a quick cold pre-wash with 1/2 cup Foca & a hot regular wash with 1c Foca & 1/2c Borax. That's what was recommended on FL's website based on our washer, water type, and skin type (need free & clear options).

@jennlin821: and others

Rather than making a whole new post, question I’ve been wondering as we are a few weeks into cloth diapering baby number two! I am adding any blankets, baby towels, and bath towels I can to bulk up my CD laundry. Do I need to add those in to the prewash? Or just the main wash cycle.

@mrsbubbletea: it's a powder-based detergent, I get it at Target. I chose it because it was inexpensive and okayed for people with eczema / allergies.

we had to bleach to get rid of stink and then used fluff love's recommended detergent and washing process for our actual washer.

@mrsbubbletea: oh bummer, that stinks! but yes, the prewash gets all the main stuff, and since the 2nd wash is on hot anyway, I wouldn't worry. I mainly stick to combining just with LOs clothes bc they're easier to hang-dry anyway (and I'm already hanging the diapers, so no need to sort) but I'd feel fine combining it with anything.

Fluff love usually recommends way too much detergent and can be really problematic!!

Your routine should be a rinse cycle with no detergent (just drain and spin, many use a quick wash--this gets out most of the pee), then a heavy duty wash on hot with the same amount of detergent you use for a regular load of laundry (I have soft water and use 1/8 cup), then one more rinse.

With barnyard stink, I'd do a bleach wash. Basically add 1/4 cup of bleach to your regular wash cycle and then do extra rinses till you don't smell bleach. Microfiber is probably part of your issue, it tends to hold stink after a while.

Please don't waste time and money on all the crazy stripping stuff!

@Becky I know you are getting A LOT of conflicting advice here. I know that all of us momma's are just trying to help. I am suggesting following Fluff Love because they are scientist momma's who have extensive backgrounds in this. So based on a few of your comments above, I'd like to add a few more things:
-Please get the test strips for you water. you have to know the hardness number in order to figure out if you need a water softener(borax/calgon) it will make a different in the type of detergent you use. If you don't soften the water, you will get mineral build up and your diapers will stink and repel. If you use too much then your diapers will not agitate propertly and the feces will not get removed.
-Please follow the directions for your washer on the Fluff Love website. Using extra rinses or not measuring your drum/getting stew will cause serious problems. Do you have a front loader or a top loader? Is it an HE?
-Bulking the laundry is extremely important. As is using the recommended detergent amounts in the index. Many people use regular old Tide, I personally use Tide Free & Gentle so that I can use it on all of our laundry.

@Mrsbubbletea I bulk with gerber prefolds (burp cloths) and flour sack towels. I received so many gerbers at my baby shower, I can keep a stash in my laundry room just for bulking. Then I don't have to worry about syncing up other laundry with the diaper laundry (can't ever get on the same page!) Don't use any towels larger than a dishtowel - nothing should be larger than a mans L T- shirt. As for bulking the prewash - I think this depends on your type of washer. I used to have a regular plan non-HE agitator top loader, and yes I bulked the pre-wash, just to eliminate the step later. But I believe if you have an HE toploader or a front loader, you shouldn't bulk until the main wash - because the wet diapers will make a difference in measuring to get the exact 2/3-3/4 full that your machine needs.

@desertdreams88 - I think you need to look up your washer on the website, the size of the load has to do with your kind of washer, not how many diapers. This is especially important for HE and front-loaders.

@lilyofthewest - bleach all the time! that's so hard on your diapers!! sounds like you need a better routine too.

I am not affiliated with Fluff Love, I just have successfully followed their advice for a year in two states with two different washing machines.

@Becky, let me know if you need more help - I'll happily answer any questions (I've done the strip/bleach once) and can ask or look up questions on the FB group for you.