It could be a virus that they keep trading off back and forth, and one that is highly resistant to your cleaning products. During a lull in fluids being expelled, get your kids out of the house for a while, then open your windows (so you don't pass out) and use a combination bleach/hot water to wipe down every surface that you can, that you don't think will be damaged by bleach. I went through this last summer, and there are also some toilet bowl cleaners that tout themselves as flu virus killers. Don't let them drink from the same cups or share food. Anything they mess on, wash in very hot water. Try to keep your house like a hospital would for germs, to keep them from picking it up again. Wipe stuff down frequently. Stick toys in the upper rack of the dishwasher (ones that won't be damaged) to disinfect them. Wash all your linens in hot water, towels, bed sheets, etc. I suspect that last year, we may have had some sort of Norovirus (it was SO contagious!) and the health department said that the virus could live UP TO 4 WEEKs on a surface. I couldn't get over that. Even if it's not a Norovirus, it could be living long enough to keep the contagion going.
After each instance of diarehea and/or vomiting, get some of that high probiotic yogurt. Their little tummies might not be back to normal, and just might be very sensitive. Although they might now have an allergy, they could have a temporary sensitivy to certain foods, such as dairy, so cutting back or eliminating those items might help them digest. (Yogurt should still be ok to give.) Kids digestive systems are more senstive than ours, they are still developing. You can also buy freeze dried acidopholous at CVS or GNC, and add a little bit to their food or something.
Good luck!