Windows pop up appears multiple time during automation execution but through manual, pop ups appears only once

Hi Team ,

I am working on automating a web application in IE and facing the below behaviour, Could you please let me know if there is some issue with Selenium webdriver 

In my application, window secuirty pop up appears as soon as we launch the url in IE. Once clicked on Ok button, it wont appear again.

But while doing the same through Selenium webdriver automation script execution, the windows security pop up appears at multiple places like uploading a file, adding a note in web pop ups etc.

COuld you please let me know the reason behind windows secuirty pop up appearing at multiple places only when automation script is executed but not through manually!