I used to get this often too until a year or two ago I started disabling mds. At it's best, there will be two mds processes running under two users; "spotlight" and your user account ("jbarely" in this case). Always looked to me like OS X was denying its self read/write access to its own folders. Can't offer a solution other than to stop mds and erase your index, then let it try to index again. That did get it to stop most of the time but only until the next time...