Some applications default to wrong monitor

Hi, i have just bought a mac pro and i'm having a problem that never existed with exactly the same set up on my g5.
i have my computer connected up to my television via a hdmi lead. so i have one monitor for working on, and then when i want to watch tv in my living room i switch on video mirroring.
for some reason now when i switch off video mirroring a few of the applications that were open seem to default to the tv screen, rather than the primary display.
at the moment i'm having to move all the application windows to the left of the screen so they overhang, so that when i switch off mirroring i can then drag them into the centre of the primary display screen.
like i said i never had this problem with my g5, so i'm thinking maybe it's a graphics card issue. is there a way to tell safari to go to the other display?
thanks

I have this with Firefox once in a while. To get it back where I want it, I open FF and drag it to the display I want it on & maximize it. Then, I open iTunes on the display I DON'T want FF in, and maximize it. Open a few tabs and close the window. When I reopen it iTunes prevents FF from opening on the other display and it goes back to the secondary.
That may or may not work with Mail

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