Hi @KevinM!
Thanks for your post! I’ll take a swing at helping you out here.
My understanding is that the CTF refinement should work more-or-less similarly for your two box sizes, provided they both have the same pixel size. Have you tried refining with either or both of the boxes?
I’m also interested in the differences you’ve observed. Could you share a few images of the differences so we can figure out what might be going on and help you interpret them moving forward?
I also want to point you to this very helpful in-depth discussion of the various effects people have observed with large and small box sizes. I frequently go back and read it myself! Why does smaller box size give better resolution?