Loading gif always visible

I had the same issue, but fixed it. Actually, the plugin meta-box isn’t structured as it should be, some of the code needs to be changed.
If you open cpt-in-navmenu.php in the plugin folder, towards the end of the file you’ll find :

echo '<div id="cpt-archive" class="posttypediv">';
echo '<div id="tabs-panel-cpt-archive" class="tabs-panel tabs-panel-active">';
echo '<ul id="ctp-archive-checklist" class="categorychecklist form-no-clear">';
echo walk_nav_menu_tree( array_map('wp_setup_nav_menu_item', $post_types), 0, (object) array( 'walker' => $walker) );
echo '</ul>';
echo '</div><!-- /.tabs-panel -->';
echo '</div>';
echo '<p class="button-controls">';
echo '<span class="add-to-menu">';
echo '<img class="waiting" src="' . esc_url( admin_url( 'images/wpspin_light.gif' ) ) . '" alt="" />';
echo '<input type="submit"' . disabled( $nav_menu_selected_id, 0 ) . ' class="button-secondary submit-add-to-menu" value="' . __('Add to Menu', 'andromedamedia') . '" name="add-ctp-archive-menu-item" id="submit-cpt-archive" />';
echo '</span>';
echo '</p>';

If you replace it with the following (only some minor changes) :

echo '<div id="cpt-archive" class="posttypediv">';
echo '<div id="tabs-panel-cpt-archive" class="tabs-panel tabs-panel-active">';
echo '<ul id="ctp-archive-checklist" class="categorychecklist form-no-clear">';
echo walk_nav_menu_tree( array_map('wp_setup_nav_menu_item', $post_types), 0, (object) array( 'walker' => $walker) );
echo '</ul>';
echo '</div><!-- /.tabs-panel -->';
echo '<p class="button-controls">';
echo '<span class="add-to-menu">';
echo '<input type="submit"' . disabled( $nav_menu_selected_id, 0 ) . ' class="button-secondary submit-add-to-menu right" value="' . __('Add to Menu', 'andromedamedia') . '" name="add-ctp-archive-menu-item" id="submit-cpt-archive" />';
echo '<span class="spinner"></span>';
echo '</span>';
echo '</p>';
echo '</div>';

added “right” to the submit button class
deleted the <img /> of the ajax gif
added <span class=”spinner”> after the submit button
the <div id=”cpt-archive”> must include all the box so the closing </div> goes at the end

that’s it

Thanks for sharing your solution!

Works like a charm! Thanks @kimtasker

Yeah it works!