I had the same problem myself. When playing DD one night I had got to quite a lengthy cutscene.(cant remember what part now) anyhow I was about halfway through the speech when my darling wife called me for tea. As I had to make a response rather than watch lots of speech i headed to the other room for my chicken salad. When I came back about half hour later I had the same screen come up stating that the storyline may be wrong. I even restarted from my last save just in case but wish I had come to the forum and searched first as it didnt matter. Just on the subject make sure you save often and if you havent got the new patch yet then get it as otherwise you could end up with resistances of minus 1 million as I did.
NIk
