On Ubuntu 11.10, I'm seeing modals from many applications show up on a different monitor from their parent application. In this example, Firefox, the application on the right most monitor, has popped up a modal dialog in the center monitor.
You'll notice that it is not just on the wrong monitor, it's also positioned horizntally against the left edge of that monitor. Vertically, it's centered.
This happens for at least Firefox, Eclipse and gedit modals. It seems like it's all applications. It doesn't matter which monitor the parent application is on, the modals are always on the left edge of the center monitor.