CNN has a typo. See the official site at:
http://www.state.sd.us/sos/results/allraces.shtml
Thune had 1,444 votes, not 144 in Bon Homme County
That was my mistake. I took the CNN numbers (which were mistaken) and ran with them without comparing them to the SD website numbers. Sorry, folks. But there were other very suspicious happenings in that county, like Thune winning decisively in 2000 and losing rather decisively this time.