My guess is it's something small that's pushing it just a little too far over the edge.
That said, it's hard sometimes to figure out what the MPAA is thinking. (I seem to remember they objected to the shot of Lurtz licking his own blood off Aragorn's hunting knife in Fellowship. They were okay with him getting gut-stabbed, arm-lopped and beheaded, but not with knife-licking.)
My guess is this R is for something involving violence toward a human. Probably the Alfrid death scene that's been rumored. The MPAA seems to be okay with violence toward orcs or goblins or trolls, but not humans.
Either that or there's a shot or two in this cut that has blood in it. They get squeamish about that. That's why there can be 300,000 decapitations in this trilogy. As long as they don't bleed. Luckily, orcs seem to contain almost no blood. Especially the digital ones.
Whatever the case, I have no doubt they'll make whatever tweaks they need to make to bring it in at PG-13. They won't want to do anything to limit sales of the DVDs and Blus.