Tools>Internet Options>Security tab, click "reset all zones to default"
MSIE has a security setting to prevent navigation into zones of lower integrity....
What security zones do your two sites map to.
To debug you web applications in IE... f12>Console tab, refresh the page to show suppressed error messages and warnings.
When asking a question in this forum for questions about html, css and scripting for website development it is helpful if you can provide a link to your website or a mashup so that we can test it.
see also
iframe sandbox attribute
Rob^_^