<<Disclaimer: Verify this information before applying it to your situation.>>
 
My doctor does say that it does make a difference as to whether you're on a
semi-gluten-free diet prior to the biopsy.  I was diagnosed last fall with CD
and my biopsy showed blunted villi with cell inflammation.  He did not
suspect celiac disease before the biopsy.  My twin sister recently had a
biopsy done by a doctor in a different state and her situation sounds like
yours.  She experiemented with gluten-free prior to the biopsy and it showed
only cell inflammation in the small intestine.  The gluten-free diet does
give her relief from the symptoms, though.
 
Her doctor labeled her as chronic duodenumitis (sp?) even with the history of
her identical twin and symptoms.  My doctor who we feel blessed to have did
his internship with Dr. Murray (Celiac specialist-Univ of Iowa) and told us
flat out that the semi-gluten free diet can mess up the biopsy because the
villi heal so quickly.
 
Both our blood work looked normal with the exception of mine which showed a
slightly elevated white blood cell count.  The anti-gliadin and endomysial
antibody test for myself were negative.  Besides having stomach symptoms, we
also have arthritic and eye conditions (sjournes syndrome and iritis).
 
Will discuss further if you'd like.  Good Luck!  We are in the process of
having our three daughters tested also.