OK, I ended up having to make new FP objects to get the alignment to work properly. I saved the settings from the previous FP objects and used these in the new.
Creating the new objects, they did not have whatever transforms were influencing the old to make them mis-aligned.
I think this is because the terrain object, the old FP trees, the FP trees splines, were all linked to a helper object. The helper object has been rotated in order to adjust the whole scene. This was adjusted several times. This transform was somehow making the FP trees mis-aligned.
I tried unlinking the terrain, the trees, etc. but it never fixed it.
Is there some way to 'Reset Transform' of the FP trees like you can with objects?