Hello TheAntiTheo,
I recommend to check at first, if the data can be properly aligned using Fisheye camera type selected in the Tools Menu -> Camera Calibration dialog.
If the images have some blank (black) areas by the corners or sides, it is also reasonable to apply the same mask, covering the no-data areas, to all the images and use Apply Masks to Key Points option in the Align Photos dialog.
Additionally, if the camera sensor locations are fixed relatively to each other, you can try using mutli-camera system approach (providing that you are using Professional edition) instead of Camera Station instances.
And can you please clarify, what do you mean, when you say "crop" in the pre-processing workflow description? Actually, applying any geometrical transformations to the original images, including rotation and cropping is not recommended, as it would affect the camera alignment step and proper estimation of the interior orientation parameters.