I found the problem. With masterpages you should use resolveclienturl ie.
<script src="<%=ResolveClientUrl("~/webapplication/js/utils.js")%>" type="text/javascript"></script>
This fixed my problem, I had a function call for OnRowDblClick which was unable to find the function using the
normal src path for js includes, once updated with ResolveClientUrl, all worked fine. Also may need
to put the scripts inside a RadCodeBlock
Thanks again