Configure tool/cvs repository trouble

[Patrick Guio]

Dear all,

I have been using the configure tool for a while together with my project
managed with cvs. Until recently I was running autoconf 2.49c automake
1.4a and libtool 1.3c and I had no problem when modifying any of the
configuration file configure.in or any Makefile.am, rerun
aclocal/automake... committing my changes, update on another and rerun
configure. Now recently I moved to autoconf 2.53, automake 1.6.1, libtool
1.4.2 and I systematically run into time stamp trouble whe doing an update
on another machine after having rebuild the system.
I can run the configure but when running make I get

WARNING: `aclocal-1.6' is missing on your system.  You should only need it
if
          you modified `acinclude.m4' or `configure.in'.  You might want
          to install the `Automake' and `Perl' packages.  Grab them from
          any GNU archive site.

WARNING: `automake-1.6' is missing on your system.  You should only need
it if
          you modified `Makefile.am', `acinclude.m4' or `configure.in'.
          You might want to install the `Automake' and `Perl' packages.
          Grab them from any GNU archive site.

If I just "touch configure" then everything is running ok again. I am not
sure which of the package is generating this trouble nut is there any
policy/strategy of using configuration tool together with a cvs
repository?

Sincerely, Patrick