Why would links not be outputting anything?

<paper-header-panel drawer mode="seamed">
	<paper-toolbar class="medium-tall menu-toolbar layout horizontal center-center">
		<img class="logo" src="assets/img/logo.svg" alt="">
	</paper-toolbar>
	<paper-menu>
		<paper-item><a href="[[~2]]" class="flex"><iron-icon icon="home"></iron-icon>Home</a></paper-item>
		<paper-item><a href="[[~29]]" class="flex"><iron-icon icon="search"></iron-icon>Parts Search</a></paper-item>
		<paper-item><a href="[[~17]]" class="flex"><iron-icon icon="communication:message"></iron-icon>News</a></paper-item>
		<paper-item><a href="[[~4]]" class="flex"><iron-icon icon="maps:local-offer"></iron-icon>Specials</a></paper-item>
		
		<paper-submenu>
			<paper-item class="menu-trigger"><iron-icon icon="shopping-cart"></iron-icon>Orders</paper-item>
			<paper-menu class="menu-content sublist">
				<paper-item><a href="[[~12]]" class="flex">My Cart</a></paper-item>
				<paper-item><a href="[[~47]]" class="flex">Order History</a></paper-item>
			</paper-menu>
		</paper-submenu>		
		<paper-item><a href="[[~7]]" class="flex"><iron-icon icon="social:school"></iron-icon>Resources</a></paper-item>
		<paper-item><a href="[[~44]]" class="flex"><iron-icon icon="social:group"></iron-icon>Uniforms & Stationery</a></paper-item>
		<paper-item><a href="[[~5]]" class="flex"><iron-icon icon="settings"></iron-icon>Settings</a></paper-item>
		<paper-item id="btn-logout"><iron-icon icon="exit-to-app"></iron-icon>Log Out</paper-item>
		<div class="copyright">
			<p>Connect v1.0.0</p>
			<p>Copyright © 2015</p>
		</div>
	</paper-menu>
	
</paper-header-panel>

<base href="[[++site_url]]" />

<base href="[[!++site_url]]" />