I have seen cracks under the nipple in mothers who position the baby too
close to the base of the nipple.  The baby then lifts the nipple with
his/her tongue to bring it into better position in the mouth, causing
the crack over time.  Try an asymmetrical latch, and see if the nipples
heal.  I would certainly look into the possibility of fungal or
bacterial infection, either of which might delay healing.  I also agree
that a reaction to something the toddler is eating is a possibility too.
Good luck with your detective work.
Catherine Watson Genna, BS, IBCLC   NYC

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