Hello kris3d,
Camera rotation doesn't matter on the processing result.
Even photos are taken in portrait orientation, they are still stored in horizontal orientation and are rotated only by visualization software (unless images are manually rotated in the editing applications, but transformed images are unrecommended to be used in PhotoScan).
In PhotoScan Workspace pane you can see image preview where width and height values don't depend on camera orientation. So in most cases cx should be greater than cy, even the image was taken in the portrait camera orientation.
Do you experience any problems with aligning original (untransformed) images?