I get identical problems when opening latex documents.  The %% comments in 
front of the Last update lines
is eaten by the macro that changes the time.  This is not the case for bash 
scripts for instance.  

This could be related to my emacs setup but the template feature just appeared 
automagically when I install
the emacs-extra package which seemed a good idea.

My version of emacs-extra is 0.1-1ubuntu1.  The fix described above is included 
in my distribution, it seems, but
the problem seems to be in the std-modes-alist definition.  Here, both the 
GNUmakefile and the LaTeX/M major
modes are missing.  Adding 

 ("GNUmakefile" . std-makefile-alist)
("LaTeX/M" . std-tex-alist)

 However, one can certainly think of many more modes which may not be listed.  
It is not clear
to me how one would automate the creation of this list.  The problem however 
seems to be on the side of the
std_comment.el  package maintainer.  The last update on that file is from 2006 
though.  An ubuntu patch for this
package?  Or maybe a user configurable variable.  If so, how to communicate to 
the user that his/her mode is 
not listed in std-modes-alist?

-- 
std_comment.el: broken code for timestamp in Makefile
https://bugs.launchpad.net/bugs/246354
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