I'm wondering if anyone has a work around for my problem. I am using a dual monitor set up with ubuntu 12.04. My graphics card is a GT8800 and i'm using the current nvidia drivers. So the problem?

When i open up a pop up window on my right screen it has a tendency to stay to the very left of that monitor. It's quite annoying as it is particularly a problem when using ardour with many plugins and pop up windows. On my left screen (which is marked as my primary monitor), pop up windows always centre themselves.

The same issue happens with the open source drivers. I don't have this issue at all if i use Gnome Shell. It's specific to Unity. Anyone know what's going on and how i can fix the problem?