If you're running your Visual Studio's internal server for debugging then firstly remove the virtual folder it insists on using.
Do this by selecting the root of your site in VS Solution explorer, then right-click and choose "Properties Window" - in the properties change "Virtual Path" from your "AppName" to /
This virtual path plays havoc with all sorts of paths..I find that if i don't make this change in VS then when I DO get all my paths working they won't work when I put the site on a live server that isn't using a virtual site.
Then set your JS reference to <script type="text/javascript" src="/js/Check.js"></script>
- using the root /
in your src.
UPDATE
If you really want to keep the virtual folder then you can try this - using ResolveClientUrl()
:
First, add Runat="Server"
to your <head>
<head runat="server" id="myhead">
<script type="text/javascript" src='<%=ResolveClientUrl("~/js/check.js") %>' />