I developped a page in Salesforce that called an inner application with this code:
<apex:page >
<iframe src="http://xxxxxx frameborder="0" scrolling="no"></iframe>
</apex:page>
This application contain some buttons that display pop-up. When I access to the application from the Salesforce page and click on a button, nothing appears. On the other side, the alert/pop-up from the calendar, managed by Salesforce, run correctly.