The motives may lie in the fact that each film has a different distributor. Flags was released by Dreamworks and Letters will reportedly be put out by Warner Bros. Of course, they were each produced by Steven Spielberg, along with Eastwood and Robert Lorenz, and each was co-produced by Dreamworks (Paramount) and Warner Bros., so the whole thing is a bit complicated and confusing, to say the least.
If Letters can gain enough momentum with such short notice, Eastwood could join Steven Soderbergh and Michael Curtiz as one of only three directors to earn two directing noms in the same year. Currently he's a front-runner for the award, which would liken him more to Soderbergh if he wins (Curtiz didn't win for either of his two 1938 noms). However, I don't imagine that like Soderbergh, Eastwood will see both of his films in the best picture category (this would put him with Curtiz on that note). Guess which one I think will be left out.