NJ and PA have reciprocity.  There must have been incorrect NJ withholdings (reflecting NJ withholdings) on his PA W2?  That may be what is triggering having to mail the return. 

With that said, there is also a NJ Form I believe you have to file, NJ 165:

Employee’s Certificate of Nonresidence In New Jersey, Form NJ-165

After attaching that form, see if it allows the efile.  I don't think it will, but give it a shot. 

You have to attach your completed PA 40 to the NJ Non-Resident return, showing that you taxed all income if you do mail the NJ Non-Resident return.