Did the stripping help at least temporarily? What did the doctor think caused the rash? Could it be yeast that's being inflammed by the diapers? My first dd had a stubborn rash that wouldn't go away for months. I tried everything under the sun and could usually manage to get it to go away completly or almost but it always came back when I switched back to cloth. Doc gave us a prescription for an anti-fungal with cortisone and it was gone for good!
Before resorting to chlorine bleach, maybe try some oxygen bleach. It's still rather controversial as it may still shorten the life of diapers but it's still quite a bit less risky than chlorine bleach. You could try boiling, but be careful as the high heat can potentially damage snaps and/or elastic. If you do I'd keep a close eye on them and keep things moving so no one diaper is lying against the hot metal of the pan for too long. If you suspect some kind of bacterial/fungal thing, a bit of a 'shock' treatment with tea tree oil might be worth considering. Up the temp on your hot water heater (maybe even dump a few pot fulls of boiling water in there if you can), soak them in the hot water and 20-40 drops of tea tree oil, strip them really well. Then hang them in bright sunlight if you can (for the UV rays) and maybe even follow up with a run through the dryer on high to remove every trace of humidity (plus the high heat can help kill anything lingering).
If you're absolutly at the end of your rope and have tried everything, it might be worth giving them a light bleaching to see if it helps. Don't use too much and make sure it's well diluted before it comes into contact with the diapers. I'd even go so far as filling the washer with water, adding the bleach, letting it agitate a little and *then* adding the diapers. Then if that does work, maybe try reducing the amount of bleach you use and how often you use it (so that ideally you might be using a 1/4 cup every month or even less if possible). Normally I'm not a fan of bleach but if it's a choice between a little bleach every month and using disposables full-time, then the bleach wins in my opinion.
Memoriesmama, just curious but wouldn't the plastic in disposables be just as bad (if not worse) than the plastic in the covers? Not to discount what you're going through, but personally I'd take another look at the diapers themselves before redoing your whole cover stash. Maybe you could even try using the diapers coverless to see if the rash still stays away. If it does then you'll know almost for sure that the covers were indeed the cause and in the meantime you're saving a little $$ on the cost of disposables. Depends on the age of your little ones, how warm it is where you live and how much carpet you have in the house but if you put enough liners in the diaper (or double diaper if you can) and maybe have her lie on a towel or something, then it's certainly doable. At most I'd buy one relatively inexpensive wool cover just to try it out to see if it really makes a difference. Although a rash that keeps coming back would cause me to suspect some type of fungal infection or maybe a food allergy/reaction. Just my 2 cents...