There are many things that can cause this problem however this KB will deal with popup overlays.
Popup overlays are those that appear on sites that look like a popup window but they are not really a popup window. Examples of these would be like going on a store's website and after the page loads up, a popup comes up that says 20% off Sale or something similar. Clicking anywhere else on the page or the X on that popup gets rid of that. This is an overlay.
To get around this in the CA Recorder, do the following:
1. Clear out the cookies and restart the CA Recorder. Reason is if you have manually closed the popups while in the Recorder, this will get put into the cookies to not display it again.
2. Re-record your script. Each time you see one of these popup overlays, click on the X manually during the recording. The click on X will get recorded correctly - as a click on a link with id 'closeButton'.
However, if you are modifying an existing script, the recorded item may get appended to the end of the script, instead of the current position. You'll need to manually drag it to the correct position on the timeline.
Once the popup is closed, it does not appear again until you delete cookies. To show the popup on every script run, add a Cookie Killer at the beginning of the script.