I run into this ALL THE TIME during the normal course of using software. I am trying to do something, then I get a pop-up about something-or-another that the developer clearly thought was important for me to see, but I click past it so I can get back to what I was doing. A lot of times is these "look at this cool new feature" kind of things - ARGH! And the worst part is, I might actually WANT to come back and learn about the new feature, but often I only get that one chance, and I'm too busy on my important task to focus on it right now.
Actually - a specific example of this just case to mind: I want to take a screenshot with Snagit - so I press PrtSn. But now Snagit pops up and asks me if I want to update. Sure, maybe I do - but not now! Now I just want to take my damn screenshot! So I click 'no.' And then I don't see it again until the next time I want to take a screenshot, and also do not want to be interrupted in my 5sec tasks with a 5min update.
Much better is to provide the information in a conspicuous, hard-to-miss area of the UI, but which DOESN'T block my workflow. Like, literally just put the text right on the form/interface in bold, red font. Like for Snagit - don't make it a popup update notification. Just put a bold/red link on the capture window and editor UI that says "Update"