A number of gnome ports use intltool for the po files, intltoolize will copy a Makefile.in.in file to the po directory when run. And is normaly run from the autogen.sh, but since autoreconf.mk doesn't.
http://stackoverflow.com/questions/10366852/autogen-sh-does-not-regenerate-po-makefile-in-in
Example: https://github.com/hughsie/appdata-tools/blob/master/autogen.sh