Understanding the problem
Inline asp.net tags (e.g. '<%= %>' are parsed at runtime when the server renders your page.
In order for ASP.Net to be able to parse documents it needs to be specified by the webserver that the extension is handled by the aspnet_isapi ISAPI extension.
The regular JavaScript files, to which you are adding asp.net code, will never run through this extension and thus will never be 'compiled' properly.
Now is there a solution?
Mads Kristensen has written a blogpost about this problem in 2008. It is still valid afaik and should do exactly what you need.
See http://madskristensen.net/post/Localize-text-in-JavaScript-files-in-ASPNET.aspx
He uses the .axd extension which is also handled by the aspnet_isapi ISAPI extension.
Another very good post which addresses the problem more specifically for asp.net mvc can be found here: http://afana.me/post/aspnet-mvc-internationalization.aspx
Hope this helps.
<%=Resources.MyMessage %>?