dual display problem - app windows open on secondary monitor

[mrhomey]

I'm running ubuntu 12.10 and a ati card driving dual monitors. Using amdcccle or amd/ati configuration app it was easy to setup dual display. Gnome is using my primary monitor properly for the main top panel and both monitors have dash on the left. Any application I launch, opens up in the primary monitor but Window popups within the application will open in the secondary monitor. How do I go about fixing this?

Thanks!

[mrhomey]

Bump

[mrhomey]

I installed xfce and don't have the window issue. I still would like to adjust window behavior in gnome though