Microsoft's investment was really just a settlement with Barnes and Noble in everything other than name.
Microsoft sued B&N (http://www.bbc.co.uk/news/business-12814018) for infringing on the patents it's been collecting royalties from Android manufacturers for. B&N then counter-sued (http://www.phonearena.com/news/Barnes---Noble-countersues-Mi...).
Once Microsoft invested in the Nook business, the whole thing got dropped. Makes you wonder if Microsoft were concerned that B&N actually putting up a fight might bring the whole of their lucrative Android licensing business in jeopardy.