When you are testing a web application that has popup windows (where the popup is a whole new browser window) you will need to make a slight change to the test script to enable it to playback successfully in Internet Explorer (no change is needed for Chrome or Firefox).
When you are recording a test against a Web application you may have to deal with a popup JavaScript confirm or alert box. This article describes the process for dealing with them.
Example of adding support for Java UI control in Rapise.