If you know that everything is pretty closely aligned and equally oblique, you can remove the obliquity information from the header using "3drefit -deoblique". You may want to do this with a copy of the datasets.

The align_epi_anat.py script takes the obliquity transformation into account to initially match the anatomical and EPI datasets. If you would like to skip that step, use the "-deoblique off" option, but it shouldn't hurt to use as long as that transformation is correct.

The AFNI environment variable, AFNI_NO_OBLIQUE_WARNING, can be used to limit some of the obliquity warnings. Given what you have said, I can not see any problem at the group analysis level, and the datasets are in Talairach space.