Howdy, welcome to the forum! As you might have already figured out, this is a great community full of people who love to help.
If possible, post the macro itself so we can take a look at it and see what might be going wrong. As one of the moderators likes to say, "If we're not testing we're guessing, and guessing often wastes people's valuable time". 
If you need help on how to post the macro, just let us know and we can walk you through it.
If you haven’t had the opportunity to read this tutorial, I highly recommend it. It will help you get the most help for your question.
Tip: How Do I Get The Best Answer in the Shortest Time?
All that being said, it's possible (I would say likely) that the window is not a normal application window, but rather a type of Dialog box (or modal system windows to use the proper terminology, thanks @ccstone for mentioning that because I was spacing the word haha). It is likely identifiable using AppleScript. Hard to say though for me personally since I'm not familiar with that app.
Also, take a look at this macro that will give you properties for all the windows in an application. If you run that macro while your app in question is at the front, and post the results here, we can likely steer you in the right direction for your needed pause action.
-Chris