I played my first runs with the stand alone (boxed) version of F3 (the one with Lunch Box and Bobble Head) + boxed Point Lookout and boxed Broken Steel. Since only the top of the red thingies is visible in this case I did not recognize them as exclamation marks back when I started the last run. I now remember seeing those red objects inside he house at the street crossing (the one with the suitcase at the entrance). I started a new run to check if the problem is part of the saved game, but the problem occurs already in Springvale. I could live with that, but when I enter the basement Fallout 3 crashes every time, so I guess there is even more missing. He is insulting me and I can see his Chinese rifle inside the placeholder. In Germantown one muty seems to be missing on the lower floors. I also reinstalled the whole game, but it did not help at all. Any help I could find on the internets talks about interfering mods, but I not have any. In Fallout 3 Game of the Year Edition (via Steam) I have the red exclamation marks (mesh placeholders) in the Germantown police station and in the Anchorage DLC outcast base (where the outcast guys fight the mutys).
