I was having this problem, flank pain associated with kidneys, a few weeks ago. I was suspicious it was because of my kidneys being unhappy at my high-protein diet. I upped my fat, water, and veg intake and only slightly decreased my meat/egg/protein intake and everything seems to have righted itself. I think my fats to protein ratio was just skewed horribly towards protein and I was dehydrated as a result, both of which makes for serious kidney pain.
Let us know what the doctor says, yeah?