Watch this screencast.  

I ran my test without any breakpoint to show what it should.  

After that, I added a breakpoint to simulate the activebrowser loses focus for whatever reason.  You will notice that by losing focus, the test does not handle my dialog box properly and promptly.  You will notice that I actually clicked it to dismiss it. 

Finally, I added ActiveBrowser.Window.SetFocus() in my coded step and reran the test.  The test promptly handles the dialog box with no issue. 
For whatever reason, this issue has been around for a while ever since releases from 2012, but I only recently figured out why my test was stopping and how I fixed it.  This is the main reason why I made all of my dialog initialization and handling to be in a coded step instead of the one provided by test studio. 

So the non-coded steps that refer to dialog boxes, add the ActiveBrowser.Window.SetFocus() on the initialization of the dialog box.  

http://screencast.com/t/R6OvdSd3