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I'm running sshmenu (3.14-1 package) on Ubuntu (Feisty Fawn). I have two monitors, running in a MergedFB configuration (shared mouse and keyboard, but separate DISPLAYs -- :0.0 & :0.1).
Regardless of which DISPLAY's gnome-panel contains the SSH Menu applet, all windows (including the menu, the alerts, the dialogs and the gnome-terms) are displayed on the :0.0 screen.
This is not the only app where I have seen this, but it was the only one where I cared ;-)
I did some digging and found this thread which suggests that this is a bonobo problem:
I was able to confirm that the applet was (incorrectly) always reporting :0.0 as the DISPLAY when it was run from the panel. The app works just fine stand-alone. I would have just used gnome-swallow, but it has the same problem.
Having absolutely no Ruby experience, I'm afraid I kludged together an icky hack using a global variable to correct the setting everywhere it was needed. It forces the windows to appear on the screen where the event that created them originated.