--could be due to celiac/gluten sensitivity. And while a positive finding of villous atrophy is the gold standard for diagnosing celiac, some people's damage is spotty enough thtat it's hard to find, or the pathologist may not have much experience in looking for that type of damage, so I would be suspicious of that negative biopsy result if you have positive blood test results.
The skin rashes, when you get them, can be biopsied to look for the tell-tale IgA deposits of dermatitis hepatiformis, which is also diagnostic of celiac.
Where do you live? It may be worth it to get to a specialty center.
I would also recommend a major look at our Celiac/Gluten Forum here:
http://neurotalk.psychcentral.com/forum13.html
--especially the famous Gluten file, probably the most comprehensive database on the subject ever devised:
http://neurotalk.psychcentral.com/thread1872.html