Your version of AFNI is fairly old. It would be worth updating (@update.afni.binaries -d) to see if that fixes the problem. Also you can add -volreg_align_e2a to make the script setup the alignment step as EPI to Anatomic.
Note that if you are using the NeuroDebian binaries, you will need to uninstall afni using apt-get and then download the binaries "openmp" binaries from this site in order to get an updated version.