Pop-up is visible in background

Hello Friends,

I am stuck on a situation automating Java Based application.

There is URL Provided to open the application and application open on Java Pluggin Installed on the system.

Problem Statement : After indicating the popup it is visible on the screen or not , but is validated successfully. If i am trying with element exits too handle the error pop up is always giving me result as true

Inshort , Pop-UP is available in the background.
If any one has experienced such problem please share your experience.

use UiExplorer for analysis and check if on this or any parent element an Attribute with name relativeVisibility is triggering on its value the display status