I have following gresource.xml:
<?xml version="1.0" encoding="UTF-8"?>
<gresources>
  <gresource prefix="/org/vala-panel/app">
    <file compressed="true" alias="runner.ui" preprocess="xml-stripblanks">../data/ui/app-runner.ui</file>
    <file compressed="true" alias="style.css">../data/css/vala-panel.css</file>
    <file compressed="true" alias="panel.png">../data/images/panel.png</file>
  </gresource>
</gresources>

And I have this into vala file:
[GtkTemplate (ui = "/org/vala-panel/app/runner.ui")]
internal class Runner : Gtk.Dialog
{
...
}

my VALAFLAGS in Makefile.am is:

project_VALAFLAGS = \
	--vapidir=$(top_srcdir)/vapi \
	--vapidir=. \
	--target-glib=2.40 \
	--gresources=$(top_srcdir)/data/vala-panel.gresource.xml \
	--pkg gtk+-3.0 \
	--pkg gio-2.0 \
	--pkg gio-unix-2.0 \
	--pkg config \
	--pkg temp \
	--pkg vala-panel \
	--pkg gio-settingsbackend-2.0 \
	$(VALAFLAGS)

valac gives me this:
error: UI resource not found: `/org/vala-panel/app/runner.ui'. Please make sure to specify the proper GResources xml files with --gresources.

I think this line in valagtkmodule.vala caused this behaviour:

codegen/valagtkmodule.vala:99 : if (ui_file == null || !FileUtils.test (ui_file, FileTest.EXISTS)) {

AFAIK, g_file_test cannot work with relative paths, but GResource loader can.(C version of this program compiles and works as expected).