It depends entirely on the pop-up (which one you are seeing), and varies from program to program and even within programs.
  Some of them are "centered to the screen" (like Lacerte sign-in).
  Others are "centered to the PARENT PROGRAM" (so if Lacerte pops up a sub-window).

Personally, I would rather that all pop-ups were done as "to somewhere that the DESKTOP IS VISIBLE" by default.  i.e. "there is nothing else in front of NOR BEHIND the pop-up, so we can bloody well see it."



Robert