Centering your datasets with that option or with @Align_Centers is often useful. I prefer the @Align_Centers method, but both work. I also set -maxite to somehting like 50 and -OK_maxite to continue if 3dWarpDrive is wavering between two equally okay solutions. I'm not sure any of this has anything to do with copying your base datasets to a new directory though. Also consider auto_warp.py for nonlinear warping and the @SSwarper script for skullstripping and aligning to some select base templates like the MNI 2009 template.