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I've got an iMac 27" i7, with a secondary monitor hooked up via its display port (adapted from a DVI cable coming out of the secondary display).

After my iMac goes to sleep, when I wake it back up, all my windows have been put on the iMac's screen. Prior to OS Lion, I had an application called Stay that helped put the windows back in the right place, but it doesn't seem to work in Lion.

Any suggestions how to prevent the windows from all being shoved back to the primary display after a sleep?

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Stay works on Lion. You may be experiencing an upgrade issue. From their FAQ:

Why won’t Stay restore my windows since I upgraded to Lion?

A number of the interface changes in Lion have affected Stay’s ability to match windows stored on Snow Leopard to windows on Lion. If you’re experiencing difficulty with a small number of windows, the simplest solution is to use Stay’s window linking feature to manually link the troublesome windows to their stored counterparts.

If you’re having trouble with a large number of windows you may find it easier to recreate your stored windows on Lion.

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