To orient one pair of photos together takes six common points. Not all photos need to share the same 6 common points. After a photo has been oriented against the current set of photos it must be scaled. This scaling requires at least one referenced point to appear on the photo being scaled and to appear also on at least two other photos in the project.
When this message appears it means that PhotoModeler could orient and scale the photos in the first list but it could not properly scale the photos in the second list to those in the first. These means that the photos in the second set do not share at least one point with two or more photos in the first set. Correcting this problem is accomplished by referencing more points in the second set of photos to points that appear on two or more photos in the first set.
You should also make sure that the photographs that do not orient properly have the correct camera assigned (i.e. the camera parameters, including zoom/focal length, match the photographs).