If you have had just a single pair not orient the problem is probably one of a misreferencing of points between those two photographs (study them with Point Audit) but the problem could also be poorly defined control points on one of the photos (incorrectly marked control or 3D definitions of control points from CTL or DXF are incorrect) or poorly defined camera parameters.
Check the references with Point Audit and check any control points using the Imports and Coordinate Systems Pane (see Control Imports) while turning off the "auto-advance" so the control points can be compared with their marks.
Another problem with a new pair of photographs that have not been successfully oriented is that the coverage might be too low. If your points in one or both of the photos cover only a small part of the photo then an instability can result which causes orientation to fail. Try adding marking points to cover more area and reference them. Even if you do not need the points for your model or measurement they might help PhotoModeler solve.
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).