Do you have any brushes filtered in the view options? I had a similar effect with hint brushes that had the broken hintskip shader on some sides. Failing that the odd shadowing indicates that one or more of the floor brushes could have become corrupted. This happened to a brush in one of my maps - it looked fine in radiant, but there were some very strange effects in game. This was rectified when I deleted the offending brush and created another.
