When running autoreconf, the script scans configure.ac for AC_PROG_LIBTOOL to determine if libtool is being used. libtool.m4 provides AM_PROG_LIBTOOL as a compatibility alias for AC_PROG_LIBTOOL, but autoreconf doesn't check for this, so autoreconf may not run libtoolize in some cases when it's actually needed.
AM_PROG_LIBTOOL is deprecated according to Libtool's documentation, and is not mentioned at all in Autoconf's or Automake's documentation (AC_PROG_LIBTOOL is). I believe the proper solution is to switch the Autoconf input file to use AC_PROG_LIBTOOL instead of AM_PROG_LIBTOOL.