It is not that uncommon for the automatic alignment to fail, particular when a larger portion of the phase and neck  is visible. One possibility is to reduce the image content by masking out face & neck regions prior to running the automatic alignment. 

You would also have more issues with alignment if the age settings between template and the data is off, e.g. adult template used with infant MRI data. The differences in size will make automatic 6DOF alignment difficult. So make sure to use the age appropriate ICBM template.

Finally, an alternative is to do the ACPC alignment manually. Several existing tools will allow you to do that. I usually use 3DSlicer load both the template and the dataset and then manually adjust the alignment transform (using the Transform module in 3D Slicer). Btw, the General Registration module in 3D Slicer is the same tool (BRAINSFit) used by AutoEACSF to do the alignment, so you could also use a good manual transform as an initialization for the General Registration module

Martin