Here is the output of the files in question. However, I figured out the problem. According to cat_matvec -help:
"The filename must end in the characters '.aff12.1D'"
I must have overlooked this when I was altering afni_proc to my batch script and my file just ended in .1D. When I change the file name to something that cat_matvec will recognize I get an output that I would expect: a matrix of 180 x 12 (180 sub bricks). Thanks for your help, this clears up my issue.

> Let's just focus on that cat_matvec command.
> Forget about
> redirecting it anywhere. You may have to alter
> 'sub' here,
> but exactly what is the output of the following
> commands?

cat_matvec -ONELINE sub_T1+tlrc::WARP_DATA -I

0.907888 0.072254 0.00889079 0.645641 -0.0497037 0.902408 0.124519 -31.8501 0.00753185 -0.0587375 0.846265 14.7383

cat_matvec -ONELINE sub_T1_al_mat.aff12.1D -I

0.988216 0.0250573 -0.00714928 3.02511 -0.0229572 0.958438 -0.273722 15.6335 -0.000665793 0.274367 0.951024 9.26318

cat_matvec -ONELINE               \
sub_T1+tlrc::WARP_DATA -I      \
 sub_T1_al_mat.aff12.1D -I      \
mat.r01.vr.aff12.1D

0.976206 0.0423889 -0.0190122 6.40158 -0.039906 0.841702 -0.524854 27.9103 -0.00682471 0.526219 0.827902 22.8861