Building with GNU toolchain

I was trying to build OpenRISC architectural simulator today. Configure task passed fine, but on the make stage I've got the following error:

configure.in:11: version mismatch.  This is Automake 1.9.6,
configure.in:11: but the definition used by this AM_INIT_AUTOMAKE
configure.in:11: comes from Automake 1.9.5.  You should recreate
configure.in:11: aclocal.m4 with aclocal and run automake again.
WARNING: `automake-1.9' is needed, and you do not seem to have it handy on your
         system.  You might have modified some files without having the
         proper tools for further handling them.  Check the `README' file,
         it often tells you about the needed prerequirements for installing
         this package.  You may also peek at any GNU archive site, in case
         some other package would contain this missing `automake-1.9' program.
make[3]: *** [Makefile.in] Error 1
make[3]: Leaving directory `/home/ant/project/or1k/or1ksim/cpu/or32'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/ant/project/or1k/or1ksim/cpu'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/ant/project/or1k/or1ksim'

After issuing aclocal command the build succeeded. WTF?
I'm not very familiar with these tools, so I googled for 'aclocal'. Here's what I found:

The aclocal program creates the file `aclocal.m4' by combining stock installed macros, user defined macros and the contents of `acinclude.m4' to define all of the macros required by `configure.in' in a single file. aclocal was created as a fix for some missing functionality in Autoconf.

It seems to me that autoconf should include aclocal functionality. I might be missing something here but shouldn't the tool be more intelligent?