Is the pop-up instantiated from your app or is it a system prompt? For example, a system pop-up would be one that prompts a user to accept notifications. Likewise, to ask the user to access your photos. If indeed there is a system pop-up appearing, KIF will not be able to access it either by tap or screenshot.
If the "context" of the Pop-up is owned by your app (sorry for the android-ism), then I suspect you should have no issue with capturing it.
What if, as a test of your theory, you went to the app code and changed the length of the pop-up display before disappearing. That might help you to debug.