It seems there is a consistency problem between the NIFTI transformations in the anat and epi datasets. While they appear to overlap initially at least roughly, deobliquing moves the two datasets far apart, and that's true for either obliquing one to match the other or cardinalizing both. The datasets show different and oppositely signed angles of obliquity for both the anat and epi.

The relatively simple solution is to avoid handling the obliquity for these datasets by either removing that from the header with "3drefit -deoblique" for both or by adding the "-deoblique off" option to align_epi_anat.py. Another option that works with this data is to let align_epi_anat.py handle the far apart datasets with "-giant_move". That expands the search to larger distances.

The obliquity warnings you mentioned in another post should be avoided with the AFNI_NO_OBLIQUE_WARNING set to "YES". I'm assuming this problem was related to the other problem using a non-standard .afnirc location, but let me know if you are still running into issues with that.