That's how it worked since Windows NT and the first dual displays back then. Not a bug.
What you find are discussions like http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=5019997 where the author of the software has to fix their applications.
Hey all... I'm running two lcds that has my desktop sctretched across both. However, everytime I shutdown or get a system pop-up, it's centered and distorted between the two monitors (as that is recognized as the center of the screen). I just wondered if there was a way to specify the center of one monitor or the other for these pop-ups? Sorry if the question is a little unclear. Thanks though