Hi Rick
FYI, 3dretroicor uses thd_timeof.c:THD_timeof_slice() to get its times. There is similar logic in thd_info.c (3dinfo) and probably in both 3dTshift and 3dvolreg somewhere, so a quick test you can do is simply "3dinfo -verb" on a NIFTI file and check the list of offset times. One of my big NIFTI datasets (straight out of to3d), appears to have no time-offset slices in 3dinfo, but it does have some if I ask for a BRIK (no .nii on the -prefix in to3d).
I'd guess part of the dset->taxis struct is lost somewhere (perhaps dset->taxis->toff_sl[]).
Hope that helps.
Fred