I was having problems with some sections of photos not aligning in a group, but they would if taken separately.
I went through the whole chunks method and had a lot of trouble getting the chunks to align properly at the end.
After not getting any responses on the forum, I asked the support email folks
They told me that if you uncheck all the photos that aligned properly, then check all the ones that didn't, and run "Align Photos" again, it doesn't erase what you had before, it just tries again to align those same photos with the existing group.
It worked great for me and I have used it several times now
No idea how you would know where to find that in a manual