One has to wonder... They have been doing a lot of miscellaneous shooting here and there, and yet they shot hundreds of hours of film over three years already. Are they adding? - changing the story from what was originally written I wonder? - or when they went to put it together, did they realize that something didn't fit right in editing and they have to re-do the same stuff?
Gandalf arrives in Minis Tirith and meets Denethor. UMMMM More coffee is needed!
In the director's interview for U-571, Jonathon Mostow talked about a scene they shot that, when previewed, left the audience wondering how Matthew McConaghey's (sp?) character knew what was going on. So they went back and added a short scene where MM was coming down a ladder, unseen, and overhearing his men talking, which worked to convey motivation. It's very likely that this type of thing is occurring with LotR.
Once that film had finally debuted, they turned their attention swiftly to the editing of TTT, and that's when the dilemmas made themselves apparent.