I am using moduleset 'gnome-2.16.modules'. gnome-vfs lists gamin a dependency.

  <autotools id="gnome-vfs">
    <branch/>
    <dependencies>
      <dep package="gconf"/>
      <dep package="desktop-file-utils"/>
      <dep package="shared-mime-info"/>
      <dep package="gnome-mime-data"/>
      <dep package="avahi"/>
      <dep package="hal"/>
      <dep package="gamin"/>
    </dependencies>
  </autotools>

When you build gnome-vfs, it should use the built gamin. It doesn't.
This is because gnome-vfs doesn't use pkgconfig to detect gamin. It uses old school 'compile a test program' method:

AC_CHECK_LIB(fam, FAMOpen,
  [AC_CHECK_HEADERS(fam.h,
    [AC_DEFINE(HAVE_FAM, [], [Define if we have FAM])
     FAM_LIBS="-lfam"]
     fs_monitor_backends="${fs_monitor_backends}fam",
    AC_MSG_WARN(*** FAM support will not be built (header files not found) $FAM_MISSING_WARNING ***))],
  AC_MSG_WARN(*** FAM support will not be built (FAM library not found) $FAM_MISSING_WARNING ***))
AC_SUBST(FAM_LIBS)

Adding the following to .jhbuildrc will get around the problem:

os.environ['LDFLAGS'] = "-L" + prefix + "/lib"
os.environ['CPPFLAGS'] = "-I" + prefix + "/include"

Should jhbuild set those environment variables for you, in the same way jhbuild sets LD_LIBRARY_PATH?