Thanks Daniel. The 3defit -deoblique and align_... -deoblique off are producing nice results.

I've got one persistent error showing up when I add the -AddEdge command line argument though. The following is the relevant portion of the program's output:

++ ###########################################################
#Script is running:
rm -f AddEdge/*
#++ Applying transformation for epi to anat for @AddEdge
#Script is running (command trimmed):
3dAllineate -base js01.anat+orig -1Dmatrix_apply 'js01.run1_al_mat.aff12.1D{2}' -prefix __tt_js01.run1_alnd_rs -input __tt_js01.run1_vr_ts_rs_ns+orig -master BASE
++ 3dAllineate: AFNI version=AFNI_2008_07_18_1710 (Apr 16 2009) [64-bit]
++ Authored by: Emperor Zhark
** FATAL ERROR: badly formed filename: -1Dmatrix_apply 'js01.run1_al_mat.aff12.1D{2}'
** Program compile date = Apr 16 2009
#Script is running:
mkdir AddEdge
#Script is running (command trimmed):
3dcopy -overwrite __tt_js01.anat_ns+orig AddEdge/js01.anat_ns
++ 3dcopy: AFNI version=AFNI_2008_07_18_1710 (Apr 16 2009) [64-bit]
#Script is running (command trimmed):
3dcopy -overwrite __tt_js01.run1_vr_ts_rs_ns+orig AddEdge/js01.run1_ns
++ 3dcopy: AFNI version=AFNI_2008_07_18_1710 (Apr 16 2009) [64-bit]
#Script is running (command trimmed):
3dcopy -overwrite __tt_js01.run1_alnd_rs+orig AddEdge/js01.run1_al
++ 3dcopy: AFNI version=AFNI_2008_07_18_1710 (Apr 16 2009) [64-bit]
** ERROR: Can't open dataset __tt_js01.run1_alnd_rs+orig - SKIPPING
#Script is running (command trimmed):
cd AddEdge; @AddEdge js01.anat_ns+orig js01.run1_ns+orig js01.run1_al+orig; cd ..
*** Can't open dataset js01.run1_al+orig
d1: Subscript out of range.
d1: Subscript out of range.
d1: Subscript out of range.
if: Expression Syntax.
#++ Creating final output: epi data aligned to anat
# copy is not necessary
#++ Saving history
#Script is running:
3dNotes -h "align_epi_anat.py -anat js01.anat+orig. -epi js01.run1+orig. \
-epi_base 2 -child_epi js01.run1+orig.HEAD js01.run2+orig.HEAD \
js01.run3+orig.HEAD js01.run4+orig.HEAD js01.run5+orig.HEAD \
js01.run6+orig.HEAD -tshift_opts '-tpattern seqplus' -AddEdge -epi2anat" \
js01.run1_al+orig

*+ WARNING: Over-writing dataset ./js01.run1_al+orig.HEAD
#++ Removing all the temporary files
#Script is running:
rm -f __tt_js01.run1*