We have had a couple reindeer cows like you describe (I know they are not whitetail).
They would run neg fecals, and cbc and chem panels seemed fine. The scours would not clear from dewormers or antibiotics.
But I do really agree with the fiber and probiotics mentioned above. The probios can be given top dressed on the feed as a supplement. Or you could bolus the individual. Does anyone out there feed beet pulp to their whitetail? It is a good fiber source.
ouldn't hurt to run a johne's test. You can do the pcr test, (believe that is the right abbreviation) it is a stool sample culture test. Doesn't take overly long to run.
Just my 2 cents.