Iframe confirm message box not working as expected

We have a requirement to implement iframe with forms to be embedded in siebel application. This form has alert in case user try to navigate away with confirm option to discard the changes and navigate or cancel navigation to further work on form until submitted. The behavior is working fine with standalone forms and if embedded in simple HTML page. However when we try to embed the same in siebel, it is not working as expected. Is there any limitation in siebel or we need specific configuration settings to make it working. Thanks in advance.