Ok here's what Im thinking, The explosions in this picture (http://www.narutobase.net/manga/Naruto/604/15) Were used to cut off Kakashi & Rin's view. But Kakashi, using his sharingan, takes on one of the ninja. Now Kakashi is good, But I dont think he can handle an anbu-Level ninja at this period. Even with his sharingan (Which he just got) He probably couldnt match the speed of whoever he's fighting. Kakashi gets led on a little bit till he starts slowing down. The ninja gets infront of Rin & quickly dodges allowing a tired Kakashi to stab her.

Now I think the reason Obito's eye is starting to hurt is because he is the original link between the two eyes.
I saw a post that suggested that it could be genjutsu, But Obito holds his left eye socket http://www.narutobase.net/manga/Naruto/604/16 (Why would genjutsu affect an eye that isnt there?)
So the two sharingan are starting to re-establish a link with Obito because they are getting closer together. And Kakashi cant see Obito's POV because he is not the owner of the eye.

What do you think?