It's a classic story telling trope for the tale to start with our heroes in deep, deep fecal matter, and for you the reader, to have no idea a)how they got there, and b)how they're going to get out. It keeps the intrigue high, there's a certain amount of satisfaction as you continue reading on through the story and see everything dropping into place, and if you do the cliffhanger well, keeping everyone on the edge of their seats as you go.
Where I do have a problem is where the in media res chapter (complete with cliffhanger!) turns out eventually to be the last chapter of a story.
That the entire story has been building up to this point, that the climax of the story just before this turns out to have nothing at all to do with the in media res chapter, and that it's all going to be resolved (probably) in a brand new story. That pisses me off.
And to make matters worse, I'm not talking about a fic here. I'm talking about an actual published book. So pissed off. So very, very pissed off.