Ok, experts, I need you.

I’ll even take the amateurs’ educated guesses. 🙂  This is a potty issue for one of my little darlings, so if you’d rather not, please don’t read on.
Organique has a problem these many days, weeks.  It is getting to the point where I’m quite worried.  She is hardly digesting her food at all.  Some days she has more ‘dirty’ diapers than not, and requires hosing-off in the bathtub to ready her for a clean diaper.  What I rinse out of the diapers looks QUITE like what was in her bowl at mealtime.  Bits of wilted lettuce, skins of refried pinto beans, bits of apple (and apple seeds), you name it, it’s identifiable.
I have severely restricted her diet to ‘good’ things; plain yogurt and banana for breakfast, scrambled egg at lunchtime, plain rye crackers occasionally, grains and beans according to the phytate-reducing techniques of Nourishing Traditions, etc.  I thought the pro-biotic action of yogurt (kefir sometimes, in smoothies) would help, but so far no real changes.  Otherwise she seems fine; not sickly, or lethargic, or anything like that.
So, Wise Ones, do you have any recommendations?  Any further ideas to try out?