The application understands that two monitors are connected and copies pixels into each monitor separately. Since the displayed images overlap, the pixels are copied twice and the image gets distorted especially when scrolling.
If you experience this anomaly only in certain applications, contact the developer of the application for a fix.
Developers can reference the following Apple Developer Services information on how to deal with overlapped graphics devices: http://developer.apple.com/dev/techsupport/develop/issue26/graphicaltruffles.html.