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I just had the same issue. I had the DSN set to use integrated MS security. (Works fine for metadata imports). I changed that to user input, saved the user/pass, and then checked fully qualified in the connection pool definition. Now I can view data and update row counts against MSSQLServer 2008.
Thanks for your input, I fixed this myself by switching to Sql Server driver, this seems to not have the strange side effect of the one I had tried originally.