According to the Autoconf documentation, there should be a make rule

pg_config.h: stamp-h

so that with the right setup around this, a change in pg_config.h.in
will trigger a rebuild of everything that depends on pg_config.h.  But
this doesn't always work, sometimes you need to run make twice to get
everything up to date after a change of pg_config.h.in.

The fix is to write the rule as

pg_config.h: stamp-h ;

instead (with an empty command instead of no command).  This is what
Automake-generated makefiles effectively do, so it seems safe to be on
this side.

It's not actually clear why this is (apparently) more correct.  It's
been posted to
<http://lists.gnu.org/archive/html/help-make/2012-04/msg00058.html>
without response so far.