Possibly related or the same as Issue 913303 - ccameron, please dup if so, Marking this one as P3. :)

Thanks for filing this. Yeah, this is issue 913303 (it was worse before!).

> Closing the certificate window also focuses the main Chrome window rather than the app's window.
 
I'm hoping to be able to get to the "unexpected refocus" soon. The incorrect anchoring is likely something we're going to have to live with for longer (in fact, it may explicit refocus to Chrome if that ends up being more appropriate).