Why the Ajax script is not running on IIS 7.5 Win 2008 R2 server?

I have a web app that works fine on VS 2013 on my development server, but once I published it on the IIS 7.5 2008 R2 server the Ajax scripts, located on my custom script file, don’t work anymore, although the other JQuery scripts that do not call Ajax do work properly. Is there anything else that needs to be done in order to have ajax working in the server? I’ve read some posts about, but couldn’t find an answer yet. I’ve limited experience in IIS and Ajax.