Re: 3 year old with strange symptoms..
I know some people use a probiotic supplement to make sure their child is getting good bacteria introduced back into their digestive system. When DS was on a higher dose of augmentin for a month we battled very loose stools, so I'd give him yogurt. But it was still a very long month and lots of extra laundry.
Another issue, that so far we've never had to deal with is C-Diff. If you haven't done so already, mention the very loose stools to your cf doctors and see what they suggest.