With the attached source code the following is rendered. The first bold line is the custom CSS file. The next one is the one rendered from the deviceResource.
<head>
<title></title>
<link type="text/css" rel="stylesheet" href="/Case13493Example/javax.faces.resource/jquery/ui/jquery-ui.css.jsf?ln=icefaces.ace&v=3_3_0_150528"></link>
<link type="text/css" rel="stylesheet" href="/Case13493Example/javax.faces.resource/themes/sam/theme.css.jsf?ln=icefaces.ace&v=3_3_0_150528"></link>
<link type="text/css" rel="stylesheet" href="/Case13493Example/javax.faces.resource/util/combined.css.jsf?ln=icefaces.ace&v=3_3_0_150528"></link>
<link type="text/css" rel="stylesheet" href="/Case13493Example/javax.faces.resource/core.css.jsf?ln=ice.core&v=3_3_0_150528"></link>
<link type="text/css" rel="stylesheet" href="/Case13493Example/javax.faces.resource/newStyle.css.jsf?ln=css&v=3_3_0_150528"></link>
<script type="text/javascript" src="/Case13493Example/javax.faces.resource/jsf.js.jsf?ln=javax.faces&stage=Development&v=3_3_0_150528"></script>
<script type="text/javascript" src="/Case13493Example/javax.faces.resource/bridge.uncompressed.js.jsf?ln=ice.core&v=3_3_0_150528"></script>
<script type="text/javascript" src="/Case13493Example/javax.faces.resource/util/ace-jquery.uncompressed.js.jsf?ln=icefaces.ace&v=3_3_0_150528"></script>
<script type="text/javascript" src="/Case13493Example/javax.faces.resource/icefaces-ee.js.jsf?ln=ice.core.ee&v=3_3_0_150528"></script>
<script type="text/javascript" src="/Case13493Example/javax.faces.resource/head-update-test.js.jsf?ln=ice.core&v=3_3_0_150528"></script>
<script type="text/javascript" src="/Case13493Example/javax.faces.resource/util/ace-components.uncompressed.js.jsf?ln=icefaces.ace&v=3_3_0_150528"></script>
<script type="text/javascript" src="/Case13493Example/javax.faces.resource/component.js.jsf?ln=org.icefaces.component.util&v=3_3_0_150528"></script>
<link type="image/x-icon" rel="icon" href="/Case13493Example/resources/images/favicon.ico"></link>
<link type="image/x-icon" rel="shortcut icon" href="/Case13493Example/resources/images/favicon.ico"></link>
<link type="text/css" rel="stylesheet" href="/Case13493Example/javax.faces.resource/iphone.css.jsf?ln=org.icefaces.component.skins&v=3_3_0_150528"></link>
<script type="text/javascript"></script>
</head>
Attached source code for test case that shows this issue.