Hello James,
trees are always challenging for photogrammetry (as they are moving and it also depends how far you are from them during capturing).
Are you using the pre-defined alignment settings?
What kind of images are you using? Are they georeferenced?
Have you tried to align all of your images in one project?
Are you trying to do the alignment in the same project as draft one?
Try to follow these advices, but for the image downscale factor use value 1.