Specifically, the error message is this:
Error occurred processing gnus.el: File error (("Cannot open load file" "nntp"))
This means that nntp.el is not in Emacs's load-path, which is easy to happen when compiling using the Makefile.
Easiest solution: set EMACSLOADPATH in Makefile (idea from Glenn Gribble <glenn@netcom.com>):
EMACSLOADPATH=/usr/local/emacs/lisp:. ELC= env EMACSLOADPATH=$(EMACSLOADPATH) emacs -batch -f batch-byte-compile
Another solution, in hack.el put this:
(defun gross-hack () (setq load-path (cons "/directory" load-path)))
Then in Makefile:
ELC= emacs -batch -l hack.el -f gross-hack -f batch-byte-compile