Sometimes autoreconf exits with an error code which is usually non-fatal. After running autorecond, run autoconf and see if that exits without error. If so, you should be set to go.
One tip -if the sources contains a script called autogen.sh it's better to run that instead of autoreconf.
If all that fails, try something like this, which is one of the ways that src2pkg trioes to resolve these errors:
# leave off '-I .' if it complains
aclocal -I .
# try either one of these
# automake --add-missing --copy --foreign
automake -a --force --copy --foreign
# run this if needed
#libtoolize --copy --force
Sometimes you need to run automake twice, the first time with no options just after running aclocal
Another thing that sometimes is a problem is that old temporary config files are still in the sources. So doing this is a good idea as well:
rm -rf ./autom4te.cache
rm -rf ./.deps
rm -f ./config.status
rm -f ./config.cache
If that doesn't work, I'd really complain to the developer.