Libtool requires intimate knowledge of your compiler suite and operating system in order to be able to create shared libraries and link against them properly. When you install the libtool distribution, a system-specific libtool script is installed into your binary directory.
However, when you distribute libtool with your own packages, you do not always know the compiler suite and operating system that are used to compile your package.
For this reason, libtool must be configured before it can be used. This idea should be familiar to anybody who has used a GNU configure script. configure runs a number of tests for system features, then generates the Makefiles (and possibly a config.h header file), after which you can run make and build the package.
Libtool adds its own tests to your configure script in order to generate a libtool script for the installer's host machine. For this you can play with LT_INIT macro in configure.ac.
So in short, if your package has configure file, run it before running Make
make distclean //clean up all the previous generated files
autoconf //or autoreconf to generate configure script from configure.ac and configure.in
automake //to generate new Makefile.in from Makefile.ac
./configure //to generate new Makefile and libtool