I had forgotten about this particular problem. A similar issue came up a few months ago.
http://afni.nimh.nih.gov/afni/community/board/read.php?1,137632,137662#msg-137662
The -omask option doesn't transform the overlap mask dataset to the atlases (or vice-versa). There are no atlases in the current distribution that are currently in MNI space, just MNI_ANAT or TLRC spaces. I'll look into finding out what is requred to transform the data for this, but in the meantime, you can download the MNI atlases from the link in the previous post. Otherwise, you could use @Shift_Volume to convert the MNI to MNI_ANAT in order to use the MNI_ANAT atlases or 3dWarp to use the Talairach atlases. Also, despite what I thought, it seems the AFNI_ATLAS_LIST variable is ignored for the omask option. Instead, use the -atlas option on the command line to specify one atlas. Sorry for the difficulty, but I'll try to come up with something more useable.
