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Hello @jackhorror,

Yes you were right shiftnav and our plugin are conflicting due to priorities of appending elements to body with jquery.

To fix loading issue, please change one setting for shiftnav from Appearance -> Shiftnav and under General Settings tab uncheck the checkbox for option “Shift Body“.

This will fix loading issue but you may find one more issue that shiftnav menu part will not animate with page. It will stay at top and blink when page is loaded. To fix it please add following code at the end of your theme functions.php file.

add_action( 'wp_footer', 'shiftnav_element_move', 1000 );
function shiftnav_element_move() { ?>
	<script type="text/javascript">
	jQuery(document).ready(function($) {
		$( '#shiftnav-toggle-main, #wpadminbar, .shiftnav' ).appendTo( '.animsition' );
	});
	</script>
	<?php
}

I have tested this with free version of shiftnav plugin. I hope this helps.

Thanks.