I had a ferret exhibit exactly the same symptoms.  Diarrhea and then
prolapsed rectum and then intermittent diarrhea again.  The vet found
two large hairballs in his stomach.  You may want to check for a partial
blockage.
 
Anecdotally it seems that kits have prolapsed rectums more often than adult
ferrets as a result of eating dry kibbled food too early.  I've not heard
of too many cases of prolapsed rectums in adult ferrets.
 
Lori
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[Posted in FML issue 2885]