Hi C.. With the rash being JUST on your daughters' diaper area... it seems more likely that it isn't a food allergy in the conventional sense (as this would more likely also give them a spotty rash on the face or etc). But a couple of other thoughts occur to me. First of course, a reaction to excess fruit, or a particular fruit, as already suggested.
The second thought I had was to ask whether the girls had a flu 3 or 4 weeks ago. Sometimes the healthy gut flora gets killed off and the result is as you describe, rash on the bottom, diarhea. Do they have a problem with gas right now as well? Should this prove to be the issue, ask your doctor about the chewable acidopholus tablets that you can buy over the counter. Works like a charm.
Has he already ruled out giardia?? Chronic diarhea is a typcial symptom. (Note that it is a parasite.) The rash could be simply from the diarhea itelf. All those caustic acids and etc.
Finally, lansinoh is probably good for the tender bottoms. But we love a product called "Bag Balm". It does not require a prescription, but you may have to ask your pharmacist for it as it may not be out on the regular shelves. Not only does it stay on as well as, if not better than, ANY diaper ointment... it has an analgesic quality. All my kids have said it makes them feel INSTANTLY more comfortable.
The reason for the funny name is that it was orginally developed for treating the chaffed udders of cows.
You can show it to your pediatrician if you have a doubts about it(because its not sold on the baby shelf), but all of ours gave it a stamp of approval.
It's also inexpensive and extremely economical. One can per kid was all it took. (Just make sure you don't dip germy fingers into it!)