Have you give "runat=server" property to your controls ? if not then give it.
try out simple script
<script language="JavaScript">
function CallMe()
{
alert("Yes..first POP up from javascript");
return false;
}
</script>
</head>
<body> Welcome to javascript example!
<input type="submit" id="sub1" runat="server" onclick="return CallMe();">
</body>